There's always the problem in game design that if you make it too convenient and remove all challenge, the game breaks down and is no fun or engaging anymore. Same goes with cheats, you have to learn to use them in a way that not takes all the fun out of a game, or if you can't, you better avoid touching them at all.
That said, bots in vanilla have only one tier, so there is no tool in the game engine to deal with the arising issue of multiple bot tiers.
I wouldn't call bot replacement a puzzle. Maybe on a small scale it is a puzzle, and such a trivial one that it is not a challenge. On a huge scale (e.g. in a hundreds or even thousands of chunks base), it is a chore, not a challenge either. It would make you have to restamp your blueprints all over the place, when you get a new bot tier, and that would only work if you preplanned for this, otherwise you'd have to rebuild that base, at which point I would rather quit or do some kind of cheat/script instead.
As for bots being "VERY smart", I wonder what makes you think that. They are not smart at all, they just pick up an item and fly straight to the target. Even to an extent of... imagine having a square lake, with an edge length higher than two times your bots range per charge. Imagine them starting in the middle of one edge, targeting the middle of the opposite edge. They will keep flying over the lake, turning back, going to recharge, then starting to fly again, even if they had a way around the lake.
I guess it's not just you, many will agree with you, many won't. Play styles differ a lot, and one player's fun will be another player's annoyance. That's what mods are for, as no game creator will ever be able to tailor a game to all potential players preferences.
As such, I'm very happy Factorio supports mods, and from what I can see, no other game does it in a better way than Factorio.
