Not taking installation issues into account, the biggest benefit of X2 over Matrix is the size of BIOS you can stuff in it. Basically, you have 1MB over 256K. For the average gamer, this isn't much a disadvantage though, as long as your modchip does what its designed for, you're covered. Most modchip now is capable of doing things that wasn't possible before and all that fits in 256k. It may be a while before they break the 256k limit, unless they decide to put everything in the BIOS, which is very unlikely.
Now, if you happen to be one of those who are very obsess with every release of BIOS available, having 1M allows you to have 4 different BIOSes (4x256). Frankly, I don't see any reason for doing that, as basically, every BIOS out there pretty much do the same thing, and offers the same capability. The more important issue here, really is, being able to flash your modchip, and both chips already came with that feature.