Finally I have internet access again. Moving and having trouble with the provider afterwards is no fun. Especially after finding out it was largely your own's fault.
@Lamabreeder: What on earth do you have against Shuttles? Why delete them? I'd much rather just turn them off so that I can revise there exact uses at a later time, uses like recon, interception, and short-range 'attacks'.
First, regarding story or "reality". Shuttles are depicted in StarTrek as small personnel transports with very limited combat abilities. On rare instances they are shown to be actually involved in combat, for instances in DS9 when they are used by the Maqis, but it is already clear from the context, that these are desperate measures, not normal space combat tactics.
In my opinion there are roughly two kinds of SciFi shows regarding space combat: Those which depict combat between carrier groups, and those which depict combat directly between battleships. StarWars is a prominent example for the former, StarTrek, however, for the latter. Using Shuttles as fighters is thus... unfitting. To a very extensive degree.
Second, regarding "game mechanics", "ease of play" or "usability". Outfitting carriers with fighters and then attacking with all these fighters during combat is tedious. It is much simpler to just build ships and then use them - with or without bombarding abilities on their own. It might make sense to have some specialized units set aside who have the ability to transport fighters - as in the regular game. But this makes only sense if this is a deviation, a variation from the standard method - again as in the regular game, where carriers are only one in a multitude of ship designs. Then you can employ carriers as means of a different strategy. The additional tediousness of building, outfitting and finally applying carriers and fighters is then offset by the fun of applying a different strategy. But if carriers are the only ship type available, then its just unecessary tediousness. As player you win nothing by undergoing the extra efforts, because it's the standard procedure and everyone does it, has to do it in order to maintain maximum efficiency. It's not about strategy anymore, about choice.
The idea to use shuttles as fighters is a neat and clever idea. But it feels a little as if it was icluded just because it was doable, not because the modpack would benefit from it. Sometimes less is more. This is one of those times.
I have nothing against shuttles, just against the idea to use them as fighters. I could ask you, what do you have in favor of this idea?
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I had another idea these days. I have not yet tested it myself (partly because I am lazy at the moment), but will share it with you anyway. I had the impression that the AI lay to much weight on ground units and built by far too much of them and by far too few space ships. You might or might not agree with this. If you do, I might have a solution. Just make every ground unit unbuildable.
Instead, use the trick you already use with the Colonists. Let's have a Small Wonder that builds a ground unit every couple of turns. Enough to protect all new founded colonies and make some ground attacks. If you want to maintain the current upgrade chain of ground units, make several of those Small Wonders, one for every upgrade level; let the older ones become obsolete once the current one can be built. This should encourage the AI to build more ships, because, you know, they really don't have much choices anymore. You can complement this with a fair sized stack of ground units (perhaps with no upkeep cost, and perhaps some very good ones among them) that is pre-given to all civilizations. Not too big, of course, because it would reintroduce the exact problem that this idea should remove.
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One last thing. I realize that my last input (the unit tweaking) was not exactly met with the greatest possible enthusiasm. I really can't and won't blame you - given that it was quite a chunk of data that I slung at you there. Since I am still interested in participating in improving this mod in some small way, I would be interested to know what chunk sizes or shapes would be more appropriate for you to actually consider.
I have the impression, however, that most efforts are currently being undertaken with regards to graphics and map. This seems to be a completely different department than the one I was adressing, and so I simply might have made my proposals within the wrong creativity cycle... ...?