Function
Size
Folk
Animation
Color
I start with function in relation to the story. For example, is this a town where the characters have their humble beginnings? Great, make it small and spread out with simple folk, maybe farming or labor happening here. Does this town have a solid history or culture? Compact, not neccisarily big or small, but definitely organized. Depending on the story importance the town has it will take on dimensions and demeanour appropriate.
Fantasy towns by their nature leave a lot to departure from realism, but I think some things are very important to have placed. If the town is a mining town, there needs to be some kind of processing facility, for example, and the folk are mentioning the local industry- but only if it's important to the story! Other things needed are a water source, a food source and places for the folk to live, work and buy things. Out in the wilderness, having salt can mean the difference between life and death... historically, anyway.
The buildings I think ought to be two tiles tall with two tiles tall of roofing on them; just my preference but generally accepted. Some RM stock animations are nice and add life to the town- like smoking chimneys and such. Don't be afraid of some critters running around, or splashing about in the local pond. Movement is the key here, use your imagination as to what might be appropriate for your town.
Color is also useful, but try to avoid monochromia unless it's part of the technique. In my project, which is based off of an existing work, the original artists made each town's buildings and folk share a dichromatic color scheme. It would be boring were it not for the fact that each town is definitely not any other town, and you can tell where you are by the color scheme. That breed familiarity with your world, which lends itself to the player's suspension of disbelief. That's called verisimilitude, and it can be acheived even with RMVX sprites!
The towns are foundational blocks to your game world. They need to be funtional and interesting all at once, and each should contain something memorable and believable, informative folk. Whatever you do, be consistent! If the folk in Southern Attleborogh are afraid of the Land Shark up north, the folk in North Judson should share that fear of the monster down south- assuming the two towns are on either side of the monster and the PC's havent defeated it yet.
Each town should have a place for the PC's to rest, resupply and gain information at the very least. New equipment should be there more often than not, or at least a place to buy things they may have skipped earlier.