This is a very interesting question to raise at this moment, considering how popular indie games development has become and how easy is to try to publish and produce your own. This of course attracted many RPG Maker users and people who never used as well. I will write down my opinions about it and, forgive-me if someone already said the exact same things.
I've been using RPG Maker for 8 years or so, already spent a lot of time on communities, playing games, giving feedback and of course, making my own projects. And there's a lot of peculiarities you can observe happening frequently, even when we are not talking about the commercial scenario. In a nutshell, the biggest issue that RPG Maker games and developers demonstrate in general is laziness. Of course, it isn't so easy to just use one word and I plan to go forward with my argument, but again, I think this sums up the general scenario.
Something very important to start with: your game's features are proportional to what your game's purpose is. You cannot say that all the games should have original and awesome art to be a good game, nor that they must have all original and innovative gameplay mechanics, and so on. Each game haves a core that will carry the most important features, some of them being art, some of them being gameplay mechanics, some of them being narrative. Of course, you can expect that all these features will have a balance between each other, but they don't need to be so sharpened as the core aspects. What I'm trying to say here is that there's no point on saying "RPG Maker Games with bad narrative are worthless" - if you are making a game focused on action, puzzles or non-linear exploration, the narrative usually doesn't matter (just an example). So the game's attributes by themselves doesn't matter, but how well they are executed on the context do.
The second part to understand is that what makes a game special is what set it apart from the others. Can you imagine a scenario where all platformer games on existence had bricks to break with your head, enemies you kill by jumping on them, coins that gives you extra lives and pipes to go down on secret areas? You can recognize some of these elements on some games of the genre, but only Mario will have them all as described. This is its identity. Same thing happens with other genres, including games on the RPG side. Here is where the two points I've made at this moment merge together: what makes a good game is how well it is executed on the given context and the identity of the experience delivered while doing it. At least is what I most believe above everything on games.
Now going to our problem: remember when I said the word was laziness? RPG maker is intuitive, it is easy to learn. But not only this, it also comes with a huge package of things already ready to use: lots of graphical assets, music, sound effect library, a huge database with enemies and heroes already done. RPG Maker already comes with a game ready to make, you just have to assemble and learn how to do so. Any first time user will be extremely happy to have so much content and will see all ideas possible to execute without much effort, just learning the basics. This is where it starts: it's easy to make, you have everything on your hands. You don't know how to do art? You don't know how to do music? You don't know how to code?! "Fear not, young aspiring indie developer. We have this done for you. And if you need more, you have whole places on the internet dedicated to provide you with more graphical assets, music and all the add-on scripts you could imagine. Go and make your dream game."
This. Having everything on hands creates safe zone where you don't really need to understand much about game design or how any of the individual parts of the process works. The principles of context quality and identity I said before will not be learned, at least not without time, study and dedication. Some people will not care or look for criticism, it doesn't matter how much ridiculous the tale they want to tell is, nor how ugly their maps are. But how can you blame them? Big part of these users are still kids or teenagers which never had any touch with game development before, of course they don't know everything and they will take the time to learn gradually. But instead of evolve with the time and develop self-criticism, some of those people will get ambitious. They will be proud of their work even if it is a frankenstein made of numerous assets ripped from what they could get, glued together and shoved on people's faces as a product. These products are the bad RPG Maker games, made without self-criticism and without the necessary time and dedication.
"But there are good games! There are good developers!", one say. And it is not wrong, they indeed exist. These are the experienced and dedicated people who started doing ugly RTP games but had the dedication to learn and become better over time. What happens is that with this experience, RPG Maker stops being enough. These people will migrate to other engines, to invest time doing art for bigger projects, they will search for things with more potential. I'm not saying RPG Maker doesn't have this potential, it does - but it doesn't so well as other alternatives, principally if what you seek is not traditional top-down J-RPGs. Again, I'm trying to paint a general picture, but there's exceptions. Some people will develop great RPG Maker games, some people will do great things without the need of having 5 years learning. But they are the minority that shines on this topic, as the reputation is made by the majority.
I think I've said enough, maybe even too much, but this is a very extensive topic. Trying to sum up: RPG Maker games are infamous in general because they are made by inexperienced people who still doesn't know how to make their games different and interesting. They make what they can do with more ease, using generic resources everyone uses and their games will be poorly executed, usually. Some of these people will ignore this fact and will try to publish their "work", while the good ones will be hidden gems buried on the communities (that are a huge niche, by the way). Most part of the experienced people will move on from RPG Maker, and the cycle will repeat - it was always like this. What makes a small difference today is what I said on the beginning: indie game dev popularity, publishers, money, steam greenlight, etc.
Just to finish, an important detail: this doesn't happen ONLY with RPG Maker and RPG Maker users. RPG Maker is maybe only the biggest example because it is more accessible than any other.
PS: I don't think that the RTP is ugly or that the default assets are bad, they have great quality. The problem is that using them imply on lacking originality, so you cannot expect to make a serious game that will be praised even if it looks exactly like another thousands made by other people like you.
The tool is good, its just that the person using it isn't that good enough.
