Well, I've run through the tutorial with Sunny with my personal companions active. We also ducked into the Schoolhouse to get in some interior combat.
I haven't seen a single issue. They fight, they follow, they teleport, they equip items, show their inventory, draw, holster, sneak, and strip naked on command. No problems moving between cells, other than the usual delays endemic to Gamebryo since the days when Oblivion was new.
I'm going to pop some ibuprofen to try to get this headache into submission. Then I'm going to reinstall my body and armor replacers. Once that thar be done, I'll install NCCS proper and fire 'er up; but considering that the base archetype for most of the features is still working properly, I'm not sure how much that'll change anything. This could once again be a case of people putzing around with bash patches and other such nonsense that are causing problems. After all, there's only been three or four reports of problems; and most don't overlap much - at least as I recall.
On the note of 1.3 itself: I only have about an hour logged on the new version, but it seems to be an improvement. I got through the entire tutorial without a crash (first time that's ever happened); and the varmint rifle is actually useful now at low skill levels. I was able to one-shot each of the bloatflies at the cemetery, where in previous versions that's taken four or five shots a piece owing to the extraordinarily poor accuracy. We'll see how it holds up, but I'm cautiously optimistic.