Just got Enemy Within and I've learned a few things.
1) EXALT operatives are suicidally dedicated to hacking the encoder. Even after I walked my MEC into it and blocked the hack they continued to rush soldiers in there. I promptly roasted them all with a flamethrower.
2) There are a LOT of EXALT operatives in every mission involving them.
3) EXALT operatives are a lot like X-COM: They flip-flop between missing a nine foot tall battlemech right in front of them to being the special forces commandos they're supposed to be. I wiped the floor with all of these guys and more that mission, and the next I lost multiple soldiers.
I once had an EXALT mission on the skyscraper rooftop construction level. The encoder was on the other side from the spawn it took several turns to get there. When I arrived the hack was in progress, they had the high ground, and reinforcements were already dropping.
It was at this point my badass covert operative made her way to a relay and hacked it, then moved in range to hack the next relay next turn. The rest of the squad overran EXALT's positions while the heavies bulletstormed there way to 3 shots every 2 turns. This continued for four relay hacks, but between the constant reinforcements, the starting distance between us, and the insane total health of the EXALT squad they still survived. As we pulled back they had multiple troops in high elevation with laser weapons firing down, and critically wounded the MEC in a single volley. I double rocketed the encoder, killing all but 1 of the EXALT troops but destroying the encoder. Most of the squad raced the last EXALT guy to the transcriber, while the medic patched up the MEC. The last guy managed to get a turn of hacking in and wound 2 operatives before we managed to take him down.
So, yeah. EXALT's effectiveness is all over the place.