(Please bear in mind I don't actually own MP-03, although I have seen a great deal of pics/video reviews of it).
The main thing everyone seems to complain about is the hip pods. I'll be honest, I think they look pretty cool- in fact, I think their biggest weakness is the fact that they didn't go full hog with the "sword-sheath" idea and actually give him swords to fit into the pods (although I would imagine budget would have prevented this from happening). They're not exactly G1 accurate, but they do give him a really unique look, and they do help with his jet mode a lot.
The other thing everybody seems to hate is the colours, for the same reason- "NOT GEEWUN ENUFF!". Myself, I think that Starscream actually looks pretty good in "realistic" jet colours (admittedly, the colour scheme is only used by a particular sub-design of F15, but there's no denying it looks cool). Also, it's such a different, unique approach to Starscream, and I absolutely love it.
From the comparisons I've seen to MP-11...I'm going to be honest, I prefer MP-03. The MP-11 is more accurate to the cartoon, yes, but let's be honest, the cartoon model was inconsistent, primitive and pretty ugly. Out of the 2 "G1" decos I much prefer the Hasbro MP-03 deco to the MP-11 colours- the MP-11 looks closer to the cartoon, but as a result has that horrible shade of flat grey plastic with no shading at all, not to mention a really hideous shade of blue. With regards to the actual physical differences, say what you will about the robot mode, but the MP-11 jet mode is patantly inferiror to the MP-03 mode. The older figure has a much, much smoother underside and almost no noticeable robot kibble/undercarriage junk. I mean seriously, look at the difference!

I do appreciate that the MP-11 is a much, much more accurate representation of the G1 original, but to be honest, I think that it's a bit too slavish to the source material to really stand out, whereas the MP-03 at least tries to bring something new to the table. Really, I'd say that MP-03 (especially the Japanese version) works a lot better if you consider it Kawamori's personal interpretation of Starscream rather than a slavish reproduction of the cartoon model. I think if this had been marketed as its own thing (Starscream: Kawamori Edition or something) rather than as G1 Starscream it would have gone down a lot better.
Anyone else who doesn't completely hate MP-03?