You can use どの by using が instead of は in your case.
どのガンダムシリーズが好きですか。
Generally, the focus of the sentence is put before が and after は. In a wh-question, the interrogative is always the most important information, so が is put after the interrogative, and は is put before the interrogative.
何が食べたいですか? (the order: the interrogative 何 --> が)
食べたいのは何ですか? (the order: は --> the interrogative 何)
Thus, you can also say like this for your question.
好きなのはどのガンダムシリーズですか。
ガンダムシリーズで好きなのはどれですか。
I like the first Gundam. It's incredible.