I see absolutely no point in multi-layering planet improvements beyond sticking things underground to protect them from planetary bombardment, which may or may not be something to include in a future version.
I don't see the point in tactical battles unless there are defensive totals for all sides of a ship, the ability to target specific systems, etc. Once you go there playing on a larger galaxy would be beyond painful. Lastly you run the risk of having a game trying to do two things and being mediocre at both of them, rather then being excellent at one.
A 3d map sounds neat for the added strategy, but i think that's outweighed by the increase in micro-management. Try to come up with a UI that has a simple method of selecting your intended cube across a big 'ole galaxy. Yikes.
carriers would be cool but as a module, not a hull.
I havn't thought about the game much beyond "how the heck do I manage this economy". So these are things i'd like to have considered, rather then suggesting them:
hurtling asteroids at colonies
planetary bombardment - large module
AI improvement that stops civs that i'm not at war with crumb-snatching planets from nations I am at war with, when i did all the work of eliminating their orbital fleet and beating their pop to something miniscule. This could apply to resources as well.
New race that has psionic powers laid out using the new ToA format.
"civ4-ish" espionage missions.
espionage treaties a-la economic and research.
rare "hero" units such as: heroic goveners, captains, fleet managers, merchants. These have no "levels" and simply provide a bonus to one or more stats (e.g. heroic leader = loyalty, entertainer=moral, etc.)
make loyalty a cool stat
"marine" module for hijacking ships.
tractor beams - the intended element is to make it risky to escort non-combat vessals by stacking them on top of a fleet comprised of combat vessals. the tractor beam pulls it off the stack.
large meteorites as an event.
Find bonus's for all ethos. Mix it up so some events its beneficial to choose good, some its beneficial to choose neutral, and so on. A civilization is old by the time they are spacefaring so have an alignment chosen at race creation. Penalize people for choosing outside their alignment. Perhaps if the slider moves out use a penalty similar to losing an election.
Labor strike as a planetary event.
'port gates. This is a type of starbase that allows a fleet to teleport from entrance to exit. Entrances and exits are set up like rally points. This speeds up gameplay on larger maps and adds a little more strategy.
terrorist attack as a random event. Spacefaring unit (including starbases) suffers 'X' amount of damage.
Ships that got blowed up real good leave space-debris on tile. This slows movement through it and can be collected for BC's (not sure about this one but worth mentioning). The 'collector' is a module a-la survey (or just use survey module i guess).
Commando ship - A cloaked ship that lands a handful of special ops to take out a random (higher % chance) or specific (lower % chance) planet improvement. Level of victims sensor research could provide a % chance to detect cloaked vessel.
well...i guess Cloaking technology. Additional sensor techs added if you did that.
Emmigration/Immigration ships - colony-type ships that emigrate 1.000 of your pop to another races planet to increase your influence over it (while simultaneously 'helping' them by increasing the pop. This means there has to be room on the planet). It might need a relations hit against you for balancing.
If you've played civ4 you've noticed when you do tech trading there is a value that is easily viewable from the diplomatic screen, to help you recognize a fair trade. I'd love something similar in *my* favorite 4X game

super-secret adult code to go from playing a 4X game to a 3X game...only when the wife's asleep.
ship parts broken down into categories such as: "wings", "bridges", etc. If you get torn on where to file one at just cross categorize it.
that's all I can think of at this time.