I'm wondering if が is interchangeable with に here. From my understanding it makes sense grammatically, but I don't know if their usage would be more appropriate in different circumstances. Please let me know if I'm wrong anywhere here.
No. Your understanding is wrong (strictly speaking, が is grammatical but the meaning changes completely). Check again what the function of が is when associated with -tai form of verbs.
Exactly. 会う and 行く are intransitive. だれ and どこ are the target, not the object, therefore indicated by に, not を. (Incidentally, だれ is the subject in だれがいちばん会いたいですか, thus, it means "Who does want to meet (someone)?".)