It's been a long time since I used TileD, so some of this may have been fixed, but I remember that if you changed the source file, updating the images in a map was a pain. I've also never gotten the hang of the ways to get auto tiling to work, I wish there were a few standards you could choose from and just point to a tile and say "this is done XP style" or "this is done Ace style". Speaking of Ace style, if you ever wanted to do sub-tiles you had to put the whole thing at half the tile size from the start, which meant that even though most things would still be the normal tile size, you would need to place each and every one as if they were four tiles. Got annoying. Also, due to the number of layers you could easily have, I would often end up with just loads of them and wanting to compress it down a bit. Doing so meant carefully remapping each thing then erasing it and got pretty confusing, I wish there was a way to select things and just cut and paste them into a different layer. Maybe that's just a holdover from me working in art programs, but I would like it. I really like the layers. The way it treated source files got a little confusing to me, often times I would start mapping something, realize I wanted to organize things a little differently or add something to a sheet and I would almost have to start over to get things sorted on the TileD file. Basically, I like to start disorganized and organize as I go, and TileD would basically require organization first to work well, but didn't force it on you. I felt a bit like I was tricked into thinking my method would work and found out later how wrong I was. RM forces the issue by limiting layers and source files, which is both a good and a bad thing in that regard.
As for RM's side,
I started a thread just to talk about it. I said a huge amount on the subject there, and there were some excellent points made, so it's worth a read if you're interested in this stuff, I think.