The Decepticons are all over the place. I just let them slide, but I like for them to be roughly in scale to Prime in bot mode (when it's "leader" guys like Soundwave, Shockwave, Megatron, and Starscream). The Autobots I prefer to be in scale in vehicle mode, but with slightly larger bot modes with clever engineering so they can extend arms/torsos. I think the Alternator and MP lines have done a decent job in making legs extend enough to get a semi-decent height out of the vehicles, while compacting enough to be in scale in vehicle mode.
Honestly, I liked MP-01/04 being roughly in scale with the 1:24 Alternators, but with the new MP-10 scale, I think they'll be in better bot-scale to each other.
Until they make a reimagined series where there's no size warping and alternate modes that aren't silly (pistol, micro-cassette, bugs), as long as they're going off of G1 alt modes and bot modes, there's got to be some suspension of disbelief. This is where I lie.
So the direction of the current MP scale (with MP-10 resetting Prime's size) is enough give-and-take for me to be fine with it (MP-01/04/05 excluded, obviously).
I do hope we get a rescaled/redesigned Megs before long, though, because I want to display them all together, and unless I get rid of MP-04 and MP-05 when the new Megs comes out, I will likely just display the 2 larger scale ones at work on my desk and keep the rest at home.