Seems odd, I don't find the PMDG 737 problematic, nor the 747 either - a pain in the ass to install admittedly - but not problematic once in there.
Still it wouldn't be the first FS aircraft which some people have problems with and some don't, I guess.
If you want a very nice, realistic freeware Boeing 737 for FS9 (early Pratt and Whitney turbojet version), then the Tin Mouse one is recommended. No CDU on it, but then again, that's like the real thing a lot of the time.
Less automation on the ATR incidentally, plus general French wierdness in the way some stuff is laid out for the CDU and AP. But it's more of a hand-flying aircraft anyway, owing to the icing regime it normally flies in. Trusting the autopilot too much is a bad idea because of that icing danger by the way. One or two real-world ATR operations require three hands, since there are normally two pilots operating it. But it is great, just watch out you don't over-rotate on take off or flare too much on landing, or you'll tail-strike it, that undercarriage is very short and the rear fuselage overhang is pretty long.
Chock