1. Taxes + Fees - This makes simple common sense and will make quick comparisons much easier, especially where taxes/fees jump because of multiple segments vs. non-stop. Back when there was one simple tax and no fees, the price quoted was the fare one paid to board the aircraft. There is no reason for that to change now that there are multiple taxes and all sorts of fees. If someone tells you that you can fly between AAA and BBB for $X,XXX, that's the amount you ought to pay.
2. DOT Vs. IATA baggage - The new DOT bag rules apply to "ultimate ticketed destination." Otherwise the April 2011 IATA rules apply. Thus, NRT-HKG on Carrier A connecting to HKG-ORD on Carrier B will have Carrier A rules apply all the way through even if Carrier A and B have different baggage rules.
A major consideration will be assuring that segments are on the same itinerary because that is what presumably lets Carrier B know that it can't collect different bag fees (or allow free bags) when accepting interlined baggage from Carrier A.
Long-term, like many rules designed to help consumers, the baggage aspect of the new disclosure rules will likely have the effect of greater transperency, but higher charges. Carriers will most likely harmonize their baggage policies and, to do so, reduce the number of free bags to an international standard. DL has already announced this for Silvers. I predict that others will follow suit over the next 9-12 months.