I am a pro who has done Infected numerous times. When fighting hard enemies like the capital ships I have nothing but the best equiped. For a challenge, when doing exploration or lower level missions, I use only white common items. For giggles, I did Infected with a PUG team using only white common MK ten items and still was owning the Borg. It is not user error. Those darn things really are too hard!
If you have problems destroying breen ships then you are doing it wrong. Plenty of other people can beat them so why can't you? I can destroy one in about 5 seconds.
also for the bolded part: infected is so simple you can three man it.
The enemy firepower is also increased, those High Yield Torps tend to become really nasty at Elite difficulty. (And it sometimes seems that NPC torps inflict more damage against shields. Never verified that, though.)
So what really needs to change is their power setup. They need to use more of them. Players have 11 BO powers, and about 7-8 Captain powers. NPCs have about 4 or 5 powers at most. They don't use them very well, either.
If you'd give every Advanced or Elite NPC at least 1 Emergency Power to Shields and cut 25 % of his shield points, you already got a more interesting combat, as you can time your buff around the EPtS (or use Subnucleonic Beam if Science Captain). The fight wouldn't overall be more difficult if you fight exactly like you did before, but it would be more interesting. Even more powers can give even more depth. NPCs will never fight as smart and effective as an experienced player, but they also don't have to be quite that easy to deal with.