On the Commander, a pretty easy house rule to back him down is "Aura bonus is Cha Mod or Class level, whichever is lower". That means a max bonus of +2 at 1st level, instead of +5 (Commander's Will feat). Plus, unless you rule differently than I would, the Commander has to pay for the equipment of his Cohort(s), which can be a severe drain on cash over time.
Sounds about right, then, with the aura bonus.
I'm still slightly concerned about getting essentially a 1st level Chameleon as a minion at 1st level. Commander even give hp bonuses for several cohort foci, so you get back most of the 4 missing hp from the lower Commoner HD at 1st level. How about this? At 1st level, a cohort's focus is fixed when you attract them. Starting a couple levels in (2nd? 3rd?) you get to reassign their focus at the start of the day (as normal).
Also, while we're talking about the Commander class, I'm trying to parse how Aid Them All works. Near as I can tell, as a standard action you make an attack roll vs. AC 10 or a skill check DC 10 to boost an ally's roll or check (or AC vs. an attack) by 2, except that instead of boosting the ally you just get an extra +2 aura bonus for the round (benefiting everyone, but not necessarily in the way you originally rolled for). There's a bit of a disconnect there, so I'm not sure I've got your intent right. Have you considered making it something along the lines of: "As a standard action, make a DC 10 commander aura check (1d20 + your commander aura bonus). If you succeed, increase your commander aura bonus by 2 for 1 round."?
Edit: Typo.
Preserving & Defiling is here. I just haven't updated the link in the WitW class yet, or created a Wasteland index. It can anywhere from +2 to -2, and if it's truly lifeless stops the character from casting at all. Most of the time, though, it ends up at -2 in those types of environments. Generally the best place to find spells/content you don't have is this place, but I also have the sourcebooks for everything if you want originals.
Thanks. I missed the preserving/defiling thread in that subforum, so I figured with the old links in the classes that you hadn't gotten to it yet. Anyways, it all check out.
One missing house rule is Flaws vs No Flaws. As well as is retraining allowed later on.
No flaws. If you really need them for your build, we can work something out.
Yes to
PHB2 Retraining, although not full on rebuilding.