Hi super_flo and welcome to the forums
There are many reasons why we don't have plans of implementing these suggestions. One of the reasons simply is that we don't have much programming work going on at the moment and these would all require that.
Another thing is that I find these new mechanics, in particular your creature specialty idea, rather complex and more in the lines of what is used in WoG. H3SW is aiming for classic Heroes gameplay where the interesting stuff is happening between adventure map exploration, city building, fighting battles and leveling up heroes. Imagine fighting an enemy mummy that is suddenly able to cast a strong debuff spell on your troops (aging, poising etc.), because it is "trained". If you didn't recognize your were fighting a mummy specialist from the hero portrait or didn't individually check all creatures to see if they were special, you would have no clue to why this mummy was able to debuff you beyond the usual curse ability. I am very much against such implementations, as I would find it annoying to have to check all creatures and their level of training before making decisions. It will create unnecessary complexity which doesn't add much interesting to the game compared to all the bothering.
I don't quite agree with your statement about magic arrow and cold ray being obsolete to lightning bolt. In most situations MA and CR are more effective in damage/spell point cost than LB. This is then of course balanced by the fact that dealing the same amount of damage with MA and CR takes longer time.
I will not say that we will not change either spells or creature specilities, but currently only some changes to the spell system may be in priority for the next release.