I think the original poster has to start with an honest assessment of what he wants. If he wants a modern, command control locomotive, then frankly, the easiest and likely most cost efficient route is to buy that locomotive new, or near new, in the configuration that you want it. We are now long past the days when command control modifications (irrespective of whether they are Lionel TMCC or DCS) are cost effective. That is not Lionel's, MTH's, or anyone else's fault, it is just the nature of the economic time that we live in. If you want to buy a loco from the 1990s that is command control, the price needs to reflect the cost risk associated with repairs or upgrades. Otherwise, like the late and great Marty Fitzhenry told me, it is an "eBay queen."
Secondarily, to the never ending debate of what will happen when command control locomotives die and there are no original boards to replace, I have two responses: Firrst, knock on wood, my command control locomotives (whether Lionel or MTH) have been very reliable. In the past two-three years, I have done some repairs on early (around 1998) Lionel TMCC locomotives. One sound unit failed, likely because I was using a ZW transformer at the time with no additional short-circuit protection, and another had a general command control failure (which turned out to be a bad ground wire). My MTH stuff is newer but generally reliable (but more like a windows PC requiring some "rebooting" once in a while. In sum, this is 25+ years of service before a problem with the Lionel locos, and when such problems occurred, they were minor. (2) Second, if they die, and the failure is more "catastrophic" (we are talking toy trains here after all, so by definition there are no serious problems), the option at that point will be to upgrade to whatever is then the new standard or relegate it to shelf queen status. Is that really any different to how many hobbyists treat post war pieces or early TMCC / command control locomotives? I know we have postwar enthusiasts even today (I always see the one guy at York who has the super mint postwar stuff, priced accordingly, but apparently really likes bringing it and packing it up every 6 months), but how many hobbyists are really still running those locomotives, after running the newer offerings? I love my postwar stuff, will never get rid of it, but the reality is that operationally it is inferior to the command control locomotives.
In sort, the sky is not falling, and this is a hobby that is a great deal of fun. And to those of you who like HO, I say that is great, HO is nice, but to me it is less visually impressive than O gauge and I will be sticking with O gauge. The fear of not being able to fix something years down the road will not ruin that fun. At some point, everything of this world will break, it's just reality.
Have a great weekend everyone. I'll be raking and mulching leaves, and then enjoying the trains with a glass of wine.