Definitely. The article is pretty subjective; I'd say there are lots of glaring flaws in Factorio. I played it for a while, stopped when I hit a major problem, but when I came back the game had changed quite a bit and I couldn't get back into it.
Flaws of Factorio in no specific order:
• The car has maddeningly terrible physics. The OP claims this yields "comic fun". It doesn't. It just means you're constantly crashing into trees and needing to repair the car.
• At some point I hit a biter nest I couldn't beat, couldn't go around (some sort of story based misson). There was NO way past this obstacle. No way to make the game easier, no way to beat them, I was even reduced to looking for cheat codes or ways to hack the game files (there weren't any). So I just dropped the game. The sudden cliff-edge in difficulty made no sense and felt like they hadn't play-tested their own game properly.
• The GUI is terrible. I have no idea why he thinks it's good.
1. Placing rails is an exercise in frustration because it's so easy to mis-align things and end up with two pieces of rail that don't quite line up, forcing you to then dig it all up and try again.
2. Placing signals and stations is an equally frustrating exercise in finicky nitpicking. There are lots of ways to set up a railway line such that it simply doesn't work, with no hints about why or what you did wrong. It feels like debugging an embedded system.
3. The article cites "TIL I learned a shortcut" being a meme - that's because the GUI doesn't help you learn any shortcuts.
4. The icons are very small yet high detail, making them difficult to distinguish sometimes. There's no way to zoom anything to make this better. The colour schemes are washed out. The art is just unattractive.
• Randomly generated maps mean you may often end up with an unusual shortage of resources, or things in weird locations.
• The core mechanic is extremely hard to actually improve at. Although I enjoyed making factories at first, I pretty quickly realised this was too much like programming to actually be enjoyable long term. Factories quickly end up drowning in 'tech debt' if you aren't experienced, so you're constantly tempted to restart levels and try again to make a more sustainable factory, but then you end up stuck again later when you obtain some new bit of tech and realise your factory is wrongly structured for the next part of the game again.
The article hints at this last problem. He says "As tempting as it is, don't restart a new factory when you want to rebuild. Just learn how to use bots to deconstruct, and fix it. It'll be more fun that way."
Er, great. And how do I learn how to use bots to do that? The game did eventually get a few half-hearted tutorials that I found actually more confusing than the game itself, but I don't recall any about bots. You quickly realise that most of the information you need to learn the game is on random user-written wikis.
Factorio has managed to get some market success despite being pretty badly built in many ways. I'd definitely recommend checking it out for the novel conveyer-belt mechanic, but if you like building games Cities: Skylines will be much more satisfying and a far more professionally built product.