Personally I think it's not so much about a specific flight school as it is about the job opportunities AFTER your flight training that matters the most...
So whichever country and flight school offers you the best work visa and employment opportunities to build up your flight time is probably the best choice for you... Since both Lithuania (I assume you're using an LTU passport?) and the Czech Republic are now in the EU at least you shouldn't have to worry about a work visa...