Alright, I'm gunna be a big presence here so get used to it. =]
I've currently used MegaTune with VEMS, MegaTune with MS2Extra, and AEM Pro with AEM'S EMS and am pretty well versed in all of them. I'd love to get my hands on a few others too but time will tell.
I've got strong opinions now on how things should be done because I feel I've seen some really bad stuff (MegaTune with VEMS) and some really nice stuff (AEM Pro with AEM'S EMS). I'll try to keep the suggestions rolling as I think of them. For starters, I'd like to elaborate on Fred's suggestion of "grabbing a portion of the map and applying a % change" (which might have been my idea to begin with =] ). There is a natural progression from that idea which would basically end up at the way AEM Pro does things. And I'll tell you, if you haven't tuned a fuel map with AEM Pro or something similar to it you're completely missing out. It is a completely different way of tuning that you get used to quickly, and should enjoy. If not, nothing of value is lost.
Here's the idea:
Every cell should be selectable using common keyboard shortcuts (holding Shift or Ctrl and clicking, or click-dragging a box area for Windows users) in any combination. Once selected one should be able to make relative changes (add/subtract discrete amounts, multiply/divide by factors), set the cell values to a new distinct value, or (and here's the fun part) do what AEM Pro calls "Calculate rows" or "Calculate columns" which takes the start and end value of a selected section of row (or column) of cells and fills in the middle cells with values such that there is a perfect linear transition in value between the first and last cell.
Something that AEM Pro has that would be a great asset as well would be a
3D map view for both fuel and spark and any other map that it makes sense for. I'm sure this is in the plans already, but I wanted to make sure it was voiced. Once again, if you haven't tuned with a 3D map, you're severely missing out.
This is a must as far as I'm concerned and one of the reasons I pleasure in tuning with AEM Pro and am beginning to loath tuning in MegaTune with VEMS, and can only barely tolerate MegaTune with MS2Extra.
I'll post some pictures of examples of what I'm talking about so you can see where I'm coming from. Pics coming tonight.