"Molthuni" is rather non-specific with respect to mechanics -- could you provide more details about what you are looking for?
Weapon training is good enough on its own, but then it can be increased by gloves of dueling. A free quicken blessing feat is nice to have too.
The lost abilities are no big deal because you will rarely have a spare swift action to use sacred armor anyway (you'll probably cast spells via fervor, use quicken blessing or buff your weapon first), and the sacred weapon damage hardly matters if you're using a solid weapon rather than some cute little dagger or whip. Channel energy is not usually useful on a warpriest other than as a feat prereq.
Edit: I'm assuming this is the Molthuni Arsenal warpriest archetype you're talking about.
Assuming you mean the Molthuni Arsenal Chaplain, in addition to what avr said, it's that many of the problems with the Warpriest were inherited via problems with the fighter, and many of the solutions to the problem with the fighter exist in the form of Advanced Weapon Training, which the Molthuni Arsenal Chaplain has access to (how much access? Ask your GM) but the vanilla Warpriest does not.
Assuming that you don't want to do something specific with blessings, and you don't want to use a normally suboptimal weapon, the MAC should be the default warpriest.