Remember this is a 4x game. You need to use strategy in depth, because everything has long-term consequences.

Research is colour coded. Red is weapons, purple is defence, blue for tech, yellow for diplomacy, and so forth.

As you research, you carry up these trees. Pick ONE weapon tree to be your main (I usually do this before the game really gets going, and only change if everyone is researching against me). And work on techs to develop your strategy, but as a rule of thumb try and keep the econ and factory techs either the same or econ ahead.

You have to build your first factory (or three) to get things going. Remember also your homeworld has a built-in farm, so an entertainment center and a market to replace the farm is a good idea. Econ centers generally take precedence over farms, unless you have a +18 uber world of death delivery.

Highlight the flagship, and click w. (I think). Or if not, click the little i in the corner, to the right of the ship name, and set to auto-survery. It now flies around getting you anomalies like cash and bonuses. Send your colony ship exploring, and try to colonise a decent planet (I rarely settle for less than PQ10). All the while, rush-buy colony ships and get them moving to colonise your empire, but be careful not to let your capital's population fall under 2.5 billion. While doing this, you use the sliders. At the beginning game rush, I normally turn social up a bit, and work at 100% capacity, while taxing for 100% morale. I lose a fair bit of money at first, but if I can survive, I'm set up.

Then evolve your playstyle. Work on weapons, or diplomacy, or economy, or tech, or whichever suits you best. You'll need some of all the trees, but generally it helps to have a decent standing army, just enough to not be the weakest.

Other than that, there isn't much more I can think of for starting the game, so just dive right in, and prepare to be beaten senseless by the AI for a while

If you break it down in stages it's easier to understand whats happening and what you should be doing in the galaxy. Most RTS games are designed to come to a conclusion in less then 2 hours, because the time contraints and attention span demands beyond that aren't realistic for a majority of players. Real Time Strategy games are almost always about building up an economy thorugh harvesting, while simultaneously building a military. In that a turn based strategy game is very similar.

Consider that most RTS' are actually RTT real time tactical games, which a strategic element really only chosable at the beginning, and later when you have to make large shifts in logisitcs, either what you build, or where you're buiding it.

So the reason you find Gal Civ2 so much slower is that it is turn-based whereas RTT is all about the instaneous respnose and reaction.

The flow of the 4X is pretty much, explore, first, find nearby resources, then expand, second, expanding to those nearby resources as quickly as possible. During the first stage you should be either committed to building up a economy or a good tech base that will allow you to ramp up the economy quickly at a later time. I almost always opt for the economy in stage one. Once you've got a few 4-8 colonies, assuming a large huge or gigantic map, then you've got a good foothold in the expansion phase, I like to use fast colony ships to move population after a colonization from the homeworld to an outlying territory and then also to keep em occupied while I'm looking for an above average planet to colonize. Once you've come up against 2 or 3 empire borders it's time to build some border patrol space craft and the expansion phase is just about over.

Now you need to ramp the economy and exploit those resources, also if you've left some of the lesser valued worlds uncolonized but they are clearly inside your sphere of influence and territory go get em before the other races do. Otherwise they'll have a logistical foothold into a deep area of your space and easier attack avenues. Once you've got your worlds moving economically you want to heavily focus on research and get ahead of the other players if possible, also use diplomacy to turn a few AI's against each other while trying to forward your own diplomatic agenda, i.e. keeping em occupied until you've got the military to proceed with the 4th X

Exterminate, find a weak or easy to take down opponent and attack. If that what your playing for have at it, if not work on your tech victory or an influence victory. But if you can achieve these then you're in good shape and should try a harder difficulty level.

Stay away from the campaign. In fact stop playing completely. read up on the game. After an hour or two doing some research come back to the game and play. Play on cakewalk in a medium galaxy with as many civs as you can and just play. Eventually everything will just 'click'.

Just a few basic ideas.

yes, the tech tree can be overwhelming at first but a few things to keep in mind. You are generally only going to need to research 1 weapons field (at least for most of the game) So its a good idea to choose that to begin with. I generally go with missiles, but, its your choice. Another general rule i tend to follow is to research techs considering both research time involved and benefit. This is especially relevant at the start. I tend to go for the quicker techs at the start, even if I'm not particularly interested in them, because after rush building a couple factories, and starting building some labs, I'm going to be able to get what seems to be time consuming ones now quicker. Another general rule, although this is much more playstyle related, is to save researching any defenses until after you know what your enemies have offensively (usually by that time the basic defenses are only 1-2 turns to research anyway, so you can catch up quickly).

Economy is really important in this game. I tend to play Federalist, simply for the economic bonus. A better economy means you can expand much faster, therefore having more planets producing more of those wonderful toys you are going to use to shoot the bad guys. It might be worth it, especially on your first few games to choose a couple of the economy bonuses as well (when you choose your race you can adjust the bonuses associated with it). Speaking of those bonuses, I find population bonuses to be particularly helpful as well, and the 1 point luck bonus is quite a bargain (helps you get those juicy 2500 credit anomolies..).

You seem to be confused as to what your scout ship should be doing while you are building that second colony ship.. Use it to scout for those juicy 12+ planets! I usually never settle anything less than an 11 (if available-- you can help this by making your planet selection 'abundant' in the setup screen) in the opening part of the game. Its well worth it to spend a few extra turns getting to a planet if its going to give you 5, 7, 10 more squares available for use.
The minimap is very useful in finding which direction to send your scouts and colonies. I will generally send my initial colony ship in the direction where there seem to be the most and most close together systems. I will send my survey/scout in the direction where there appear to be more clusters further out.. (empty space tends to contain more anomolies-CHA-CHING!)

Rush buying your initial 2 factories on your home planet, and (if you can affort) at least one per new planet is also an extremely successful tactic.

The other choice you are going to have is which ethical alignment you wish to be. When given the ethical choices for planets, your playstyle comes into consideration. Do you want to be friends with everyone? Do you want to be friends with some, but not all, do you want to crush all who challenge you? Personally, I pick the evil choices as they tend to give much more immediate bonuses- and getting ahead early is key! However, if you are in a smaller galaxy, or surrounded by others, you might want to choose good or neutral, as it will give you less enemies to fight.

Finally, boost your military rating the cheap way! As soon as you get space weapons, design a Tiny hull ship with no engines and 1 weapon, and make it the first build priority for every planet as soon as they get a starport. Just build 1 per planet and put it in orbit of the planet (if you are really eager, rush buy it). Military rating calculates looks at how many of your planets are considered 'defended' but doesn't neccesarliy look at the quality of defenders. So you can make the AI more reluctant to attack you buy stationing these otherwise useless craft around every planet. Just remember to change your build queue so you don't build more than 1 per planet.

Keep in mind (especially as you play more) you want to have a general idea where you want to go from the beginning- a warmonger, a tech-head, a diplomat, etc. Your choices should reflect that choice, although as the game plays out you may find another choice to be better and if so, you can change.