igoryoufool: Messiah came out in 2000 - by that time, both Thief and Metal Gear Solid had been released, both much better stealth games.
Totally different kinds of stealth games, however. Those games are based on view and camouflage, Messiah like Hitman is basically based on disguises and stealth based on disguises is far more complex as that kind of stealth requires the AI to act accordingly to your behaviour in their view. And the fact that even the newer Hitman games still struggle with that mechanic, tolerating behaviour that should instantly turn them hostile or making enemies see through your disguise for behaving like the AI characters, just shows how complicated this kind of thing is. Especially the first Hitman, released the same year as Messiah, had strong issues of this kind and yet people seem to be far more forgiving in that case. And Messiah even has additionally factions which makes things even more complicated and justifies the occasional flaw in the system even more, IMO. (and yes, Hitman 1 officially does have factions but IIRC they never turn hostile towards each other ingame thus eliminating the issue you're criticizing about Messiah)
And well, in Messiah most of the time it's logical that NPCs turn hostile as soon as you draw your gun. Of course the developers should have introduced an exception to this rule when a combat situation between the factions arises but one of the reasons why they forgot / didn't manage to do this was most likely because there's so few situations where this would have been necessary and introducing this exception might have broken the basic mechanics. And the fact that you can still easily beat the whole game, despite this obvious flaw, is enough of a reason why you can't call the game itself broken.
igoryoufool: As for GTA - if I commit a crime, the cops attack me with varying levels of viciousness depending on how much havoc I cause, while the unarmed citizens run away. Nothing illogical or unpredictable in that.
Well, it's illogical that AI controlled characters can do the same stuff as you do but the cops behave totally differently towards them (they can run over someone right in front of cops and the cops don't care, IIRC), basically the same thing you accuse Messiah of. Still I don't say that GTA is broken because of that. And sure, in GTA the issue is less obvious but I can't even honestly say that it's less harmful to the whole game. There's been quite a few situations in the GTA series where I failed a mission because for some reason the cops treat me much worse than anybody else in the universe.
igoryoufool: Edit: The reason I'm attacking this game is that I really wanted to like it
Yeah, I thought so. Oh well, I still liked it and always felt that it received too much criticism and will defend it for pretty much ever. Especially since it's one of the *very* few games based on disguises and the most original one at that (a cute cherub taking over people and wreaking havoc? awesome! :D).