If you want my honest opinion, modability isn't, or shouldn't really be a priority, except for very popular AAA games. The simple reason is that there are not enough modders to go around, and even very popular games like UT2003, Homeworld 2 and Call of Duty only have a few good mods with a dedicated team. Lesser known games, if you will forgive the term (which includes 95% of all games), don't usually get enough talented and dedicated people to make it worthwhile.
You could say that games like Starshatter and FS2 are the exception, but I would say that because a) they have been around for many years, and so have built up a strong community over time and b) are a niche genre.
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Ok, as for actually helpfull suggestions...well, I would say you pretty much have it covered. For me, it's not so much a matter of how much features you have, but how well they are implemented. Some sort of mission selection, even among 2 or 3 choices at a time sounds like a good idea (if you have ever played Freedom Fighters you know what I mean).