Use whatever can best tell your story. Or in most cases, easier for those involved to produce.
Some RPGs that employed a side scrolling view:
Valkyrie Profile: Lenneth by Square Enix/Tri-Ace
Valkyrie Profile uses the side view to great effect by emphasizing action platforming in exploration. The element of verticality and jumping was at the time, not something you saw out of a lot of JRPGs, and it was a welcome break from the standard maze faring JRPGs usually provide, while still remaining true to its DNA by providing what was still a turn-based battle system.
I don't mind action platforming, but I've yet to find a tight and responsive one made with RM. I may not be looking hard enough.
Phantom Brave by NIS
The
Phantom Brave one is a bit of a cheat. The game actually employs a top-down isometric view of the area in battle and a side view for cutscenes, but I do still believe this game is worth mentioning. Compare the cut scene screen shot above to the in-battle one below:
In battle, character sprites are smaller and their proportions are squished. This is likely for screen economy or so they can keep more of them visible on screen, which is important when players constantly have to survey the map to evaluate their next move. The bigger sprites in the cutscene afford players a more detailed view of the characters capable of producing more nuanced, expressive movements.
Rival Threads: Last Class Heroes by Kontrabida
Likewise, this closer view of the game world affords the opportunity to depict more details into the environment. It's beautiful and easily sets your game apart from most other RM games.
It won't be easy, though. We don't really have graphic resources that fit the style, so more likely than not, you're going to have to produce most if not all of the graphics yourself or find someone who can. I honestly don't like mapping on RM. Without parallaxing or a lot of work outside of the editor anyway, something just looks really off with the final product. That's just me, though. I work with a bunch of artists that may have never touched an RPG Maker in their lives. A number of them found the size limitations stifling as well so they instead requested we somehow tweak how the game is presented. We all pretty much agreed on just doing it this way because it was more convenient for us.