Thanks for asking for our input. It is a great game overall, and the following suggestions are meant to maximize enjoyment of playing the game, rather than to be taken as a negative assessment of the existing game. Well except for this first one.
* Please Please Please fix the save game bug that does not allow the loading of certain saved games, esopecially autosaves, at a certain point. I have yet to finish a new gaem started in 1.5 because of this.
1) An active perimeter defense option for militar starbases that would allow them to attack any enemy ship that came within range (this wold necessitate that the enemy ship be able to defends itself and fire back from up to 8 squares away for fairness in this case which might be difficult to impliment). Perhaps a specific set of upgraded long range attack modules that would do the same thingbut at a much lower damage rate, the AI doesnt get to fire back and is subject to one round of low damage per turn spent in the starbases' radius.
2) Trading weight revalued. You've heard all the arguments for this in other posts so I wont go into detail, suffice to say currently the AI values certain techs far to highly (iewont trade one colonization tech in exchange for 3 in return) under 1.5X but planets and treaties are valued far too low (ie 2 class 13 planets gets an AI offer of 267bc) for realisim.
2b) AI planet valuation should take into account proximity to Empire. I have seen the AI, on occasion, not sell, at any price, a mid PQ world on my doorstep, about to be won over with influence, that was SEVERAL sectors away from its next nearest planet.
3) Not every AI planet should have a starport, some AI worlds class 3 have the colony center, a starport and a farm... which I suppose is indicative of a larger AI building priority assessment problem where it doesnt tailor planet's build cues to the individual circumstances of each planet.
4) Allow AI players to colonize class one planets
5) Have planet class reflect the END value of all terraformed squares, not the current value. It is hard to plan strategy for empire building ifI have to wait untill all my planets are upgrades fully before I see which ones are goign to be PQ 8 and which ones are going to be PQ 18.
6) Allow users to delete core templates and have such deletions only apply to what is visible on their ship template/build screens (so the corresponding AI player still has those templates to choose from but the player does have to obsolete all those designs everytime a new tech is researched)
7) Improved AI ship component utilization. Mostly for speed/sensors. The AI does not tend to maximize the potential of engines and sensors, to the point of not even researching the technology. It is common to see late game AI ships with a speed of 7 and the standard sensor range, while I, having researching most of the miniaturization techs, which they also don't make a high priority, are able to have twice/3x the speed and double sensor range with the same attack/defense values.
8) Borders should be invioable, if a peace treaty exists between species, except for trading freighters.
8b) Don't make peace treaty automatic upon first contact. A peace treaty should be somethign you ahve to research/earn, rather than automatic. Statuts after first contact would be neither at war nor at peace. Exchanging peace treaties would improve relations but bar you from entering their space to explore anomalies/get resources, etc.

) Your borders, area of influence, should start off much smaller than they currently do, one sector, max. They should grow with time. If we JUST got hyperdive, and haven't explored ANYthing, how can my area of influence extend to a place I haven't even been yet.
9) Galaxy map/explored area should be tradeable.
10) A map editor, preferably accessable in game, should be implimented post haste. I am a big fan of self-customization, and feel such a tool is invaluable for longevity of game enjoyment.
11) Institute a selectable 'repair' command for ship with the toggle on the ship info screen next to guard, sentry, and the like.
12) ALL improvements should destructable, including superprojects and galactic achivements, and subsequently able to be rebuilt elsewhere.
12b) Certain improvement effects should be altered. Ie, the glactic resort should apply either A) empire-wide, or

be much higher bonus for the planet. Harmony crystals, ultra spices, frictionless clothing, and VR modules should increase in cost, and benefit from first available to last. Ie Harmony crystals should cost (for illustration purposes) 100 and give a 10% boost to morale (as they are the first available morale tradegood) while VR modules should cost 1000 can give a 40% boost to morale (as they are the last available morale trade good).
13) Graphics should be scaled in the 'Stats and Graphs' section of the Civilization Manager to allow for a viewing of all the stats at once, rather than going back and forth with the slider to view military, then technology, for each race compared to you.
14) If allied with AI A and at war with AI B, should be able to ask AI A to send ships to specific sector, or attack specific planet of AI B.
15) Economic Tile Bonus, as suggested by others, seems only fitting as there are concurrent bonus tiles for every other improvemetn type.
16) Multiple 'special' module ship placement. Thus a constructor (with 2-3 construcotr modules) would be good for 2 or three improvements, or a miner (with 2 mining modules) would be be doubly efficient, or a trader (with 2 trading modules)doubly profitable.
17) Have computer conduct all automoves to destination at same time, rather than individually one by one. In mid-late game I have 10-20 starports churning out ships to rally points every turn, and it takes forever for the computer to cycle through each move before my 'turn' is over.
18) Planet invasion,, if successful, should not kill 100% of the enemy's population of that planet (maybe 60-80%). Not only is every citizen of a planet not a soldier, but at a certain point of combat losses nearly every enemy surrenders.
19) Great idea, copied from previous post:
Maybe make PQ 0 planets something more than just space takers (I don't say that they should all serve a purpose and yes some should just be there to take up space but I believe there could be some use to them, possibly blow them up to reveal a resource or investigate certain planets to uncover bonuses)
20) Great idea, copied from previous post:
Instead of the UP deciding on their problems at random or letting some more influential civ choose for them there should instead be a sort of raffle that lets the winning civ choose from certain categories (so it helps to have influence but it won't guarantee you anything)
21) A MUST HAVE, copied from previous post:
An option to distribute races evenly across the galaxy (or, like star distribution, a bunch of settings: exact symmetrical distribution, loose distribution, random distribution).
22) The Jagged Knife event should only take planets with less than a certain approval rating, and then perhaps only a percentage thereof.