Command upgrades make economic sense only in two situations:
-- You have a fairly expensive conventional locomotive that is in excellent condition (a brass engine, or a large steamer such as a Proto-1 Cab Forward
-- You can do the work yourself and you get a great deal on used parts or a donor engine.
I've done both. On the first point, I upgraded an old Weaver brass John Wilkes to PS/2 with an MTH kit. It runs beautifully and was worth every penny of the cost and every minute of the several hours I spent on the conversion. This was a couple of years before Weaver came out with the very similar Black Diamond engine with TMCC. I have a number of older brass 3rd Rail locomotives that I plan to upgrade whenever I have the time.
In the second category, I have upgraded a number of older diesels that are not available in specific roadnames with modern electronics by swapping the body from an older unit onto a newer chassis with modern electronics. If you can get both engines at a good price on the secondary market, this works out well. Among others, I have done this with an MTH Milwaukee Road H10-44 and a Milwaukee Road DL-109. In both cases I was able to put together a second, conventional unit from the leftover parts and sell it for enough that the net cost of the conversion was much less than that of upgrading the older engine with an MTH kit.
Of course, you can always upgrade a locomotive that you just plain like and it has sentimental value. But that is a decision based on personal value, not economic value.