Difference between merged and split

There's no difference in content. There are the same number of games.

The difference is that for the fully merged set, each game will have all of the ROMs (parent ROMs for the 'main' game, clone ROMs for all the various revisions/regions, and common ROM files that all of them rely on) in one zip archive instead of several different archives.

In a split set, you'd have the ROMs required for the main Street Fighter Alpha 3 in one archive (sfa3.zip), but then you would also have several different .zip archives containing all of the ROMs required for the other versions of that game (sfa3b.zip, sfa3h.zip, sfa3u.zip, sfa3ud.zip, sfa3ur1.zip, etc).

It really is down to personal preference.

Reference

 * Wikipedia, the free encyclopedia