Lets take credits as an example, as well as a rarer resource like Cryotic.
For the maximum reward in the smallest possible timeframe, Index is unbeatable. If you want to farm Cryotic, farming Lith Excavs for Cryotic is way faster than anything else I've found. Or, you could farm some quick cash, and get a little Cryotic on Heiracon at the same time. Pretty much the choice is yours. I've never sat down and tried to work out the exact time required to make X amount and then cross-checked them both, and honestly, I couldn't give a fuck. Sometimes I want Cryotic, sometimes I want cash, and sometimes I need both.
Most of the time, I'd rather run an hour of Index, get my cash, and then run Lith's for Void Traces and Cryotic. What I don't want to have happen, is needing to run Index for the best cash, the best xp, and the best Endo drops.
If they boosted all credits in missions to be on par with Index, then credit farming wouldn't be a thing, it would devalue credits to the point no-one cared about it. Alot like nano-spores and alloy plates. Maybe I'm wrong on this one, but I think that would be an incredibly bad thing to do.
I dislike Hydron xp farming, it's boring as hell, and everyone expects to get carried (or outright afk), so there's no-one to carry so shit takes longer than it should. I'll still do it on occasion to get a frame rolling, but with the MR system boosting mod capacity, I really don't need to these days.