I don't know whether to agree or disagree with that. On the one hand, it's quite obvious monsters and PC's fundamentally didn't follow the same rules, as just by way of one example the difficulty of using PC's as monsters often shows. Indeed, each of the types of monsters followed its own rules, and then each specific monster usually made exceptions to the generic 'ooze' or 'giant' or 'dragon' or 'vermin' template in various ways. Granted, at the system level monsters and PC's used the same base concepts - hit points, saving throws, skills, attacks, damage, etc. - but that's true of most systems. It's a rare system that has hit points for PCs and a wound track for monsters, as that sort of inconsistency tends to mean that the system is more complex rather than less.
I guess I don't understand how you can both feel constrained and also feel that you had a high level of customizability. When I opened the 3e MM, the first thing that struck me was just how much of the customizations I had felt compelled to employ to provide challenge for higher level PC's (doubling or tripling the HD of a monster, for example) was explicitly validated by and encouraged by the system.