Well since you asked...
Although I can't pretend to be an expert on the history of Czech Aikido my time here has allowed me to meet some committed and talented martial artists.
The dojo where I currently train/teach is Aikikai based having been started by Valiant(sp?) sensei in 1990. Although Valiant has since returned to France the yudansha he trained have taken over the running of the dojo. The building functions solely as a dojo which means a full slate of classes is available.
Although I never had the chance to meet Valiant sensei I can't but admire the attitude he instilled in his students. The combination of strong aikido and tolerance towards other martial arts/forms of budo mean that we have a strong flow of visitors who come to practice or teach. Just this year we have organised a seminar in Krav Maga, have invited an instructor to hold regular classes in tai chi and have a resident (long term I hope) teacher of Kyokushin karate at the dojo.
My aikido experience before coming to the Czech Republic was Yoshinkai based (which seems to make me a minority of one over here)but the guys don't seem to mind - they fall over the same way Yoshinkai folks do. The longer I train over here the more I am convinced of the absolute truth of my teacher's words when he said (I paraphrase)..' there is only one Aikido'.
To cut a long post short I'd just like to add that if any of you out there are planning on passing through Prague bring your gi, it'll be fun.