One of the knocks on X-ships, at least in SFC (and SFB, too, I suppose), is they are lazy ships to fly. They are so powerful (mostly) that they aren't as much fun, especially for those who love the challenge of power management. Does that mean they aren't fun to fly X vs. X? Not necessarily.
Making a very large list of X-conversions from late-era ships seems to me to amount to a total mod along the lines of a TNG mod. There's certainly a place for that, but considering the prevalent attitude toward Xes, it does not really belong as part of a D2 server that progresses through eras. It's been shown in the past that once campaigns reach the advanced era, most of them suffer huge losses in player numbers, leaving the X-fans left to finish off a campaign that no longer has any sort of player balance resembling the field up to that point.
However, limited Xes per SFB make sense in that they are expensive to build and maintain, and many designs would be nearly identical, meaning you don't need as many. Also, they served a purpose in SFB of countering the Andromedans. For anyone wanting to do an Andromedan campaign, it makes sense to have some Xes to fight them with.
In D2 terms, unless you stop non-X production altogether, Xes will still be matched against "normal" ships and vice versa, whether PvP or solo or coop vs. the AI. As such, the Xes scream for some competitive balance.
Anyway, this is my take on the issue at the moment. It is informed by some past experiences and player feedback. Until I see indications Xes are thought of in a different light, it would be irresponsible of me as an admin to ignore players' preferences. I do think there can be room for Xes in some campaigns, but not unless players try them and find they add something without taking away much more.