I'm no NR expert at all, but one large problem with the ICE upgrades is that they have to be put on rezzed ICE. This makes total sense in terms of gameplay, however crucially the runner sees it happen and so there's no surprise. Even without the issue of ICE destruction, this problem pretty much renders ICE upgrades uninteresting or weak I think.
It seems to me that the possible uses (and their value) for the current flavours of ICE upgrades fall like this:
1. Add strong/exotic effects to ICE - e.g. brain damage (though potentially a lot more interesting stuff). This is generally pointless as the runner will see it coming and so just not run it if they can't handle the effect (though perhaps they will for a hail-mary run if this still won't stop that, but then it's likely too late anyway). Even things like choosing the ICE subtype, or borrowing subs off other ICE or doing RSVP stuff etc. - anything like that the runner will just see it coming, calculate the price/risk and run/not run.
2. Make taxing ICE more taxing - more subs/more strength on already passable ICE. This has value (I'm no expert though), but does it run the risk of your taxing becoming too taxing and becoming blocking ICE instead, thereby defeating the object of the point of it being taxing? Perhaps taxing ICE could do with a taxing upgrade later in the game when econ has increased, but then...what about just more ICE?
3. Making an open ICE closed - by which I mean they could break it before and now they can't - e.g. too strong now, or they need a breaker, or perhaps it's too dangerous, basically the runner stops running the server as they can't get in. This has value, but often your ICE is carefully chosen and so when the runner stops running it they'll stop hitting those subs. Again, is this what you want? Perhaps, but I would think it's a niche use case of you having porous ICE and no blocking ICE for your servers, and you need some blocking ICE quick and cheap. Perhaps you would be better served with some actual ETR ICE instead? Maybe the fact that it costs 0 is useful? Dunno.
I think people's suggesting of the upgrade making the ICE un-trashable (or at least harder to trash) is perhaps one of the most useful things it could do. In a similar vein, make it so that it can't be moved around by runner cards, or perhaps that it cannot host any cards (parasite, Knight etc.), or can't be un-rezzed. Perhaps the most useful things that can be done are simply to prevent the runner doing things to the ICE that are not encapsulated in ICE vs ICEbreaker interaction, because anytime you get to ICE vs ICEbreaker on rezzed ICE you both know what's going to happen already. However, this just leaves upgrades as counters to other cards really, which can be useful for sure but, I dunno that sounds a bit lame to me.