Gramsci’s Kingdom has an excellent post on the politics of international football federation membership applications and their effect on Kosovo. In short: if you opt for Kosovo, you’ll probably never get the chance to play competitive games against the big countries.
The rules changed after Spain effectively vetoed Gibralter’s application, and now you need UN membership to become a UEFA member. Russia will almost certainly veto Kosovo’s UN application. And to join FIFA you need two years’ membership of a member confederation, so unless Kosovo ‘does an Israel’ and joins CONCACAF, they won’t be playing full internationals.