You could argue that the Croatian independence referndum was also illegal but Croatia is an EU member today.
No, you can't. Croatia had every right to leave Yugoslavia, in accordance with Yugoslav Constitution from 1974. Every Yugoslav Republic had the same right: Croatia, Slovenia, Bosnia, Macedonia, Serbia and Monteblack in spanish.
Kosovo's secession from Serbia was illegal, because Yugoslav Constitution never allowed for such possibility for Kosovo which was one of the provinces of Serbia. And this is exactly the argument the Russian's are using (and rightly so) - if EU and USA allowed something for Kosovo and set such precedent, why would it be impossible for Crimea? Most of EU countries (except for few dealing with secessionist movements themselves - like Spain for example) recognized Kosovo's independence, and USA did it in the first place. Shit, NATO led by US even made it possible in the first place by bombing Serbia & MNE into submission and making Serbia withdraw all the troops from Kosovo.
Also, one could argue that Crimea's referendum formally took place, no matter how ridiculous it was, while such referendum never took place in Kosovo. Not to say that huge majority of Kosovo's population wouldn't support independence, but formally there never was any kind of vote, they just said one day Kosovo is now independent and USA and bunch of countries immediately recognized it as an independent state.