Some of it is admittedly that Maelstrom just made more sense in that location, so there's kind of a subconscious issue there -- I also hate that they blocked up the opening for FEA, although that's more about experiencing it from the pavilion and not the ride itself.
I think the advanced AAs in Frozen actually... detract isn't the right word, but I think in some ways they draw attention to how barren the rest of the ride is because they're very high quality (absent the terrible faces) and then everything else is just kind of there (or not there in some cases).
Expectations probably play a part too. Maelstrom didn't get 60+ minute waits, and I never expected it to be more than what it was. The first time I rode Frozen Ever After, with the long waits (I had FP+ so thankfully I didn't waste my time waiting) and the fact it was based on one of their biggest hits in a long time, my reaction was "that's it?"
All that aside, just watching the straight comparison Maelstrom feels like a more cohesive experience, even though it was random in places too.