I too didnt like the idea of Stormies been minions, they are an iconic part of Star Wars, and I never understood why the "Emperor's elite" as they are called in the beginner box were portrayed and bumbling idiots who couldn't hit the broad side of a barn in the movies.
The whole "should stormtroopers be competent or bumbling screwheads" is another long discussion that has shown up on these threads (I come down on the competent side, BTW).
BUT because they are minions does NOT mean they fall into that latter 'bumbling screwhead' category.
There seems to be this assumption that, because something is listed as a minion, it cannot be dangerous.
And this is total crap.
The reason they created the "minion" type NPC is to easily manage a large number of combatants on the field as much as or more than it is to give the players a way to feel good about dropping enemies easily (this absolutely was the purpose of 'minions' in some other games, such as those created by shoreside dwelling sorcerers). You can run stormtroopers as individual henchmen in your game if you want, and more power to you. The problem, however, is that is REALLY going to slow your game down because you're making A LOT of separate rolls: one per ST per round.
If you want your STs to be tougher, then make them tougher. But don't think that the only way to make them tougher is to make them henchman, because this is, again, nothing more than Bantha pudu. You can make them tougher and still minions by increasing their damage or abilities or just adding in boost dice or wounds or soak or whatever, but still treat them as minions!
Personally, I have no problem running Stormtroopers as minions because they always show up in groups. I'm totally comfortable interpreting the profiency dice they get for being a group as a representation of all that time they spent training to operate as a cohesive unit. Really, when was the last time you saw a single stormtrooper fighting a group of PCs? They practically always show up in groups.
They travel in packs because thats how they can be most effective!
My advice is to pump up the individual ST minions, continue to treat them as minions, and operate them in moderate to larger sized groups. I can't speak for anyone else, but I doublt that many tables have really found that a group of 4-5 lower level PCs can easily outgun a company of STs, led by an ST seargeant. I have seen a dozen STs, split into 2 groups of 6, and played intelligently, mop the floor with some new PCs, and even some more experienced groups.
The inevitable counterpoint to what I've said above is that lone minions don't get proficiency dice on their rolls, which means they suck. I can show you simuulated data that shows that to upgrading proficiency dice doesn't really affect the outcome of the roll as much as you think it would. So even though your STs aren't rolling yellows (by themselves), they can still throw down some serious firepower.
tl;dr version: In this game system, 'minion' does NOT neccesarily mean 'incompetent', 'cannon fodder', 'weak'; instead, 'minion' simply denotes a type of NPC that can be easily managed as a group, despite what previous game systems have done.