Regarding X-ships, do as you will, since it has been adequately demonstrated that the appearance of the MIRV at it's original OP time ends servers. Hence FS should seek to ensure that his list meets GSA style requirements while having playable ships for all empires. Then let server admins choose when they want their servers to end with their own individual shiplist adjustments. What I would like to see is, after a little bit of tweaking, that OP+ becomes the default (stock) list that all admins will start with (but not have to stick to). GSA requirements will mean that all the current X2-ships will have to stay in essentally as they are though, for those great 400 advanced games.
To achieve an X-ship balanced server which includes Taldren X-ships as they are now is a nightmare I would wish on no one because you may get applause for trying but very little satisfaction for the majority. Still, it will be an excuse to get online to play it so that it can be criticised.
As for Kzinti ship balance (and Rom for that matter) I don't like it when people say they have to have more power (or PD) to be able to play the game, when what they mean is that need more of factor x to survive a battle with empire y from the other side of the Alpha Quadrant. It is not simply a case of Kzinti were not meant to fight plasma (which is what the extra power is needed for) but that most of the empires were meant to fight certain other empires in certain timeframes. Add this to the fact that while there is balance built into GSA matches and SFB scenarios, nothing is built into D2, except bugs. I also think the ISC have more to complain about regarding fleet restrictions, but then I also think the ISC prior to late era is an abomination anyway.
Some Kzinti problems could be addressed by a few rules though (or actually lack of). Fleet limits for example, if Kzin need fleets of small ships to compete in PvP, then allow it for Kzinti players, but don't design a server where fleets of drone ships run amok, taking territory at a parsec a minute. And make the small ships expensive enough so that when the solo enemy CC knocks out one of the little droners then it is worthwhile, and not just one more mission to replace it. I don't see a problem with empire specific rules as long as a player only needs to know about half a page (to print out and keep handy if they need to).
Anyway the latter two paragraphs are about server design, which should come after this shiplist project which is the issue at hand. Once you have the default shiplist, design the server then go and make mods to the shiplist if you want to, so as to achieve the objective of the server.