I think that Clickteam has generally been evolving over years, and since they've used the same old source code then they've sort of bolted on new features.
Apparently MMF2 had a fair bit of the code redone but it still wasn't a total recoding as people seem to think. I asked on their forums and they said they basically had only recoded the Corel bits and weren't about to rewrite over a million lines of code.
Whilst this makes MMF more stable than Construct i think Construct does some things better, like global events etc.
Clickteam admit they can't even add 'else' because of the way their event system works. And i think their graphics engine has given them a lot of problems, now they're trying to update to things like Hardware Acceleration.