Couldn't have said it better. Beware, spoilers ahead.
My main issue with A4 is that it has utter predictability in plotline. Yes, it follows logically from A3, but too logically. At least in A3 we didn't know the Vahnatai did it until later in the game. This was the "big surprise" in the game.
A4 has no mistery. By the time we reach Formello, we have a pretty good idea what is going on and who is behind it all. Motrax's Lair pretty much confirms it and seeing that good old Rentar is behind everything is not a leap of imagination at all.
Ironically, when I said this to Jeff he reacted quite offensively to any challenge in his paradigm.
Pity, because there were so many avenues to persue such as the Slith Wars with real motivations other than they are evil and savage. The Darkside Loyalists worked quite well and had more focus been on them all the better. Betrayal by a powerful wizard, unconstrained ancient Vahnatai magic, some new ominous threat, etc. could have been potential avenues. However, Jeff picks 'Kill Rentar' which is the most obvious and storyline that has been the butt of so many joke BoE scenarios.
Not to say A4 is all bad; there are good parts, but plot is not one of them.