DisclaimerFirst of all I'd like to say I love this game and I have over 500 hours on steam, with a further couple of hundred hours not logged. That said I get a little triggered when everyone on these forums (and the steam forums) praise it as if it's the best game ever with no flaws, so I have compiled a list of some of the flaws. The list is somewhat ordered with the worst flaw first. Please don't take this list as a personal attack.
tl;dr version (please read the full text before getting angry):1: There's only a handful of buildings, with few or no side-grades.
2: The beacons and requester chests pits creativity against efficiency.
3: The "win" condition is totally misplaced.
4: The biters are confused and almost a scam if considering the promos.
5: The lazy reskins are weird to me.
6: It's basically just a bunch of recipes and adding recipes is not very advanced.
Full version:1: There's only a handful of buildings, with few or no side-grades. The 3 assemblers and 3 furnaces are straight upgrades, so can be considered as 1 each. The assembler, chemical plant, refinery and furnace while doing the exact same thing doesn't compete with each other because each recipe requires one and exactly one of them. This makes for a rather linear and boring experience. The only side grade in this game is your choice in power. The way solar panels, accumulators, boilers, nuclear reactors and transportable steam work and are balanced against each other is sublime. Imagine if the 3 assemblers and 3 furnaces could be changed in a similar way, from boring straight upgrades to a strategic choice, how much more interesting the game would be.
2: The beacons and requester chests pits creativity against efficiency. Even with the lackluster content you can still make some beautiful and creative designs. However the two mentioned things severely hamper this because the implicit goal of factorio is to be efficient:
-Requester chests kills belt logistics: Every recipe can be created with a requester-asember-provider chain. If you are not using this chain for everything but perfectly straight belt lines you are making your factory less efficient.
-Beacons force perfect grids: The most efficient way to produce things is to have 8 beacons per assembler and 8 assemblers per beacon. This can only be accomplished by placing them in parallel straight lines. Any attempt to use direct insertion breaks the pattern and thus cannot be used. Another design, efficient in another way, is to have the maximum 12 beacons per assembler. This can also only be accomplished one way which is already a boring square. On top of this each square has to be placed in a perfect grid else you pay for more beacons than you have to.
3: The "win" condition is totally misplaced. You win the game so fast that the people who only play to the "win" won't experience much of the game unless they go out of their way to do so. For the rest of us the "win" is totally meaningless, because it is just a science pack among others, not more significant than when you set up purple science. From my perspective it would be better to just remove the "win" prompt and treat it like any other infinite builder game.
The greater point is about pacing, and it ties up all the first 3 points here. While people who play to the "win" miss out on game content, so do those of us who play continuously. The beacon problem (above) is not a problem if you only play to the first rocket, because almost none of your assemblers will have beacons and modules. Neither is the first point a problem, because at least straight upgrades change what you can do in your designs, and the refinery introduces multiple outputs, which is sufficiently different to feel fresh the first time you unlock it.
If the intent is that we should only play to the "win" then I question even more the asking price of €25, because there are few random factors and even fewer branching and exclusionary choices that makes doing the first 6-10 hours over and over interesting. The most common argument I hear in defense of the price is how many hours you can spend, but even though your very first newbie play-through may take more than 10h you really can't spend that many hours in the pre rocket phase unless you are interested in speedrunning. Therefore I conclude that continuous games are essential for the value of the game, and therefore point 1 and 2 are problematic flaws.
4: The biters are confused and almost a scam if considering the promos. It seems to me that the developers have changed their view on what they wanted the biters to be from their original plans, but just left them in limbo. Almost every aspect of this enemy is simple and boring. There is lots of creativity when it comes to weapons, but because the enemy is so boring this is sadly almost wasted effort. I could explain why they are boring, but clearly the direction now is to just reduce their presence in the game, and it makes me wonder why we can't just get a "/c for all revealed chunks if entity=enemy do destroy" bomb.
5: The lazy reskins are weird to me. Compared to the other flaws this is a very minor one. I'm talking about many things only differing in color. The circuits, science packs, inserters, belts, chests, modules, 3 of the ores, etc. All several versions but with only a color differentiating them. The game is so incredibly polished in so many other aspects, so I don't understand why this is.
6: It's basically just a bunch of recipes and adding recipes is not very advanced. I could add hundreds of new recipes in the blink of an eye, and since the game is based almost solely around these recipes I can expand the game massively this way. The only effort is in balancing these recipes to make an interesting experience. This is mostly a problem in relation to the price, as being small and simple isn't a bad thing in and of itself. I'm not saying €25 is too much (although it may be considering the no sales policy), but some people suggest it is worth even more than this, and there is no objective ground for that.