90% of my maps are made in GIMP and integrated via parallaxing soooo...uh...I go nuts?
I guess parallaxing itself is the answer to the question, i'nt it? RPG VX Ace's mapping system made me pull my hair out (literally! I've got scars!) so I started parallax mapping to solve it. Made lots of pretty ones. Got tiresome. Even with the much wider sense of freedom, it takes a lot to make one map and keep it 'fresh', as you say. Really, if you use parallax, there's an unspoken expectation that it should be elaborate and decorated, unique and fresh since you're not working within the restrictions of the original mapping system. Basically, I just end up recalling my favourite elements of RPG dungeons and towns and find a way to recreate them. I'll toss in things that aren't even related to the main plot, like elaborate market squares and an interactive bell tower because that's what this kind freedom gets ya.