Sorry, this will be a loooong post

Did you look for any programs in Prague? Because my advice would definitely be go to Prague. I recently moved, but I lived there for 6 years and I came there to study at Charles University so I can tell you it's a great place to be a student. Also I know a tiny bit about the CG industry in the Czech Republic. Here's some reasons to go to Prague;

International Community: Prague's full of international students, travelers and expats and there's so many interesting people there. Also it's easy to meet people and it's a very friendly place once you find your feet. If you're looking to move abroad in the future you're far more likely to make useful connections, friends and broaden your horizon than you would be in Brno where fewer people go.

Cultural Hotspot: Prague's the most beautiful city I've been to and it's full of culture, there's always art shows, poetry readings, film festivals, galleries on every street corner and the place is crawling in artists, photographers, film makers from both the Czech Republic and all over the world. It's a very easy place to get involved in the artistic community and meet like minded people.

Inexpensive Capital: If you compare it to the rest of Europe it's quite cheap, you can spend a lot of money in Prague but you can also live very cheap as a student and still enjoy life. I lived in student accommodation when I first got there, it was pretty scary but it was just 2000 cz crowns/month and you can still get a beer for less than 20 crowns. The nightlife in Prague is great and it's a city that never goes to sleep, you have 24 hour bars and 24 hour trams so even if you live a bit out of the city center you can always get to where you're going. Also you've got an airport and you can pick up pretty cheap tickets (as Prague is a tourist city you have direct flights everywhere in Europe) and explore other places where you might want to move. If you're in Brno this gets a lot more time-consuming and pricey.

Job Opportunities: If you need to work to make some extra cash while you're studying it's a tourist city so there's many bars and restaurants where you can get a job. These things are always easier in a capital city than a place like Brno.

For 3D there's also a few studios in Prague, these guys developed FurryBall which is a pretty big deal and it's very possible that in a few years time the Czech Republic will have more of an impact than today. There's also a lot of innovation in architecture so some good small archviz studios in Prague which might offer a way to get a foot in the door and some work experience/ internship which would be helpful to go abroad with later. I highly doubt Brno could compete here, so if you can find a similar program in Prague I think you're in a much better position to start a career in this field later and move abroad.

Cheers,
Nilla