In real life we see teams bringing upgrades which don't always work out for various reasons, do you think there should be something in place that either reduces the effects of upgrades your designs or just straight up makes the new part worse then what already exists. This could be related to staff or facilities, whilst it would be very annoying when playing the game, I think it would add some realism to it

Edit: also on a slightly different note, should facility levels reduce over time by a level or 2 just to show technology evolving, so once you've maxed your facilities they aren't maxed forever with the occasional refurbishment, you'd actually have to keep upgrading them