My advice to anyone looking forward to Kosovo joining Montenegro in the ranks of European football: don't hold your breath.
Yes, it's true that some pretty dodgy FAs have made it into FIFA in recent years. But these for the most part have been concentrated in Oceania and CONCACAF, who have been keen to up their numbers in order to get a regular World Cup spot (in the former case) or to bolster Jack Warner's political position (in the latter). In Asia, there has only been one slightly dodgy addition (Palestine). In Africa, where they are fairly mindful of not screwing around with post-colonial territorial settlements, nothing of the sort has happened. In South Africa, political stability has meant the issue hasn't arisen.
In Europe's case, it's been a different story. The break-up of the Soviet Union and Yugoslavia have created a number of new smaller states which have been eager to take up sporting nationalism. A number of legally legitimate if geographically ludicrous micro-states (Andorra, San Marino, Lichtenstein) which have also chosen to take up membership. None of these has been particularly contentious.
The exceptional case is the Faroe Islands, which was granted FIFA membership in 1988 and UEFA membership in 1990. The Faroes have a significant degree of autonomy, but they are legally part of Denmark. Their membership has led to all sorts of claims by other sovereignistically-also-rans to get a place in UEFA and FIFA.
Of the various suitors that subsequently claimed a desire to join, Gibraltar had the best case. But Gibraltar had one major drawback - namely, that its legal status was contested by the Spanish, who had no desire to see Gibraltar's international standing confirmed by any international sporting bodies. So they threatened UEFA: if Gibraltar plays, we don't - not in any UEFA competition. Since Big Cup would look a bit strange without Real Madrid and Barcelona, UEFA caved. Gibralta have twice successfully appealed this refusal to grant them status at the Court of Aribitration for Sport, but UEFA continues to stall.
The Gibraltar case rang alarm bells at both UEFA and FIFA, with both suddenly realizing: maybe this recognizing every two-bit organization with pretenstions to sovereignty just so we can say we have more members than the UN isn't the greatest idea since sliced bread after all! At which point, they changed the rules. And it's these new rules that Kosovo has to deal with.
Let's start with FIFA's rules, the relevant sections of which in Article 10 read:
(i)Any association which is responsible for organizing and supervising football in its country may become a member of FIFA. In this context, the expression "country" shall refer to an independent country recognized as such by the international community.
(ii) Membership shall only be granted if an Association has been a member of a Confederation for over two years.
Ok, then, over to UEFA, whose Article 5 reads:
(i) Membership of UEFA is open to national football associations Members situated in the continent of Europe, based in a country which is recognised by the United Nations as an independent state, and which are responsible for the organisation and implementation of football-related matters in the territory of their country.
Note the subtleties here. The wording does not require that only one FA per country is permitted - that's how the Faroes and the four home nations get to stay. But it does require that the state in which one is based must be not just "internationally recognized" (the FIFA standard), but a member of the UN.
This is where Kosovo will take it in the neck: UN membership requires Security Council approval, and the Russian Federation - which for obvious domestic reasons is not keen on legitimizing the rights of ethnically homogenous enclaves to unilaterally declare independence - seems set to veto Kosovo's membership application. No doubt in a decade or so, a compromise will be found to allow this new country to join, but until then: no UN membership. Which means no UEFA membership, which means no FIFA membership.
There is a possible escape loophole, though I suspect Kosovo would be unlikely to use it. There is nothing stopping Kosovo from joining another confederation with looser membership qualifications. Among the likely options: CONCACAF has no geographical restrictions on membership at all while the Asian and Oceanian confederations will take members from outside their areas provided, with the only stipulations being that members cannot be in two confederations simultaneously and that their membership be in accordance with FIFA statutes. Crucially, Kosovo passes the second test, since FIFA requires not UN membership but "recognition from the international community" - which Kosovo has, at least from the US and most of the EU.
OFC and CONCACAF are probably non-starters for financial reasons. The AFC is more proximate and hence more affordable. But for obvious political reasons, Kosovo has a pretty large incentive to portray itself as "European", and an AFC membership may clash with this.
Still, participation in international football is an important demonstration of sovereignty, and the Kosovans will want to start as soon as they can. How this story plays out is anyone's guess, but early entry to UEFA is probably the least likely scenario.