Yeah, MapTool suffers from feature 'rot' - every good software project starts out as something small that morphs into something that's too big. MapTool is too big - its great that its configurable but only if you know its configurable and where to configure it. It happens to every software project, unless you prune it from time to time.
Going to disagree with you here.
In fact, *this* is exactly how MT should function (and does function for most users who stick with it):
At first, we just used the basics -- shared map, PC tokens, monster tokens as HP bags with no functionality tied to them, and minimal VBL. Then we started getting into macros and line of sight stuff, and more elaborate maps. Next came a friend in the group writing up a framework for porting 4E character files into MT. But all this took years to happen.
And today, it functions the same way. You don't have to know how to build (or use) the "Bag of Tricks" to use MT. It's just an option.
The problem isn't that it has too many features, it's that all of those features aren't necessarily *simple* to use. And anyone coming into the program needs to know that they need to learn how to walk before they make the jump to light speed (I mean, they could end up flying into a star or something).
Take something as basic as "targeting". In MT you have to build macros for it. In Fantasy Grounds you can target by "Ctrl-LeftClick". So in MT it isn't as "easy", but boy can you do way more with it--you can pull up range based, sight based, token type base, or name based targets... just to name a few qualifiers.
So, as far as I'm concerned, while it might be nice to have a simple "Ctrl-LeftClick" targeting option in MT for users that don't want to learn MT's MacroScript, there would be mass revolt if you tried to "prune" the program to that level of simplicity.
I do believe that too much of MT's power is gated behind the macro language... but that's where the expertise and momentum seems to lay with the current crop of developers. My guess is that they'd argue that it wasn't worth their development time coming up with a non-macrocentric method of targeting since macros can do it... so they turn to other features more interesting to them. And, thus, MT remains more of a souped-up muscle car than a slick looking, under-powered, sports car.