To be honest, I actually prefer buying separately.

1) When i was a kid, my mother gave me Brawl. Dude. Brawl. This amazing new Decepticon tank guy. I was what 9 years old? I know every inch of that toy. By the time I could make Bruticus, I'd poured over all the limbs (I got Onslaught last). Each Combaticon toy has so much personal history. Even as an adult, I find myself taking one toy out of a boxset per day so I can drink in each one's majesty.

2) Sense of accomplishment. Adult collectors (mostly) have the money to go buy a boxset whenever we want. Sure, we might be bringing a packed lunch to work for a week or two if we buy on impulse. And there are exceptions (I saw Dinoking on sale once, $A2,000!). But we can buy the whole box simply enough, if we really desire. The sense of accomplishment isn't there. Well, maybe in finding Dinoking (if not in opening up to realise you paid $333 a pop for repainted Pretender Monsters).

3) You can pick and choose. Take the Liokaiser boxset with that horribly shoehorned Dezarus and 4/6 of the Breastforce as an example. I'm a big fan of the Breastforce combiners but the Dezarus core just didn't work for me. I bought the set and sold Dezarus cheap... now I have four nice limb bots without collector cards.

4) Kinda ties into what you said above about replacements. I like Combiner Wars Brawl (and the character) enough that I have both Bruticus and Brawl on display. I didn't have to go out and buy two Blast Offs to do it (only to go buy the shuttle version also!).

Your pros to the boxset are valid (along with the awe-inspiring box filled with TF goodness, something of a counterpoint to my first point). But yeah, separately works for me, even if Hasbro's distribution model doesn't always.