I actually thought it was fairly straightforward, though I never did figure out precisely why certain factions like G22 were involved (though the full dossier entry for Alpha Protocol has given me some... interesting ideas about their possible origin). Well, straightforward in the sense that yeah, it's a tad convoluted at the beginning of each specific operation but by the end you have a fairly clear picture of what you were trying to accomplish. Italy was probably the vaguest initially, as all you know is there's an Al-Samad cell active but not why or how that relates to the PMC that is secretly evil. Still, easy enough to figure out what was going on, and you'll know why if you hack the various laptops you find in the last mission.
If you'd been playing the game in small chunks though I can see how that might make it harder to keep things straight. I can't say I ever got any of the various characters mixed up though, they're not especially "samey" after all. Especially the female characters (all of whom you can sleep with, you actually get a perk for doing just that which gives you an additional 5 AP points. Well, all the female characters who talk anyways.).
