Well, here's my diddy on the matter. I think I'm going to be the only one to agree with you that the EToP is better than PokeSupe, on certain aspects. First of all, there are major differences between the two that doesn't quite make them comparable. EToP is based on the anime while PokeSupe is based on the game. EToP also relies heavily on the reader watching or knowing about the anime. PokeSupe, however, creates its own story that doesn't require game knowledge and actually strays from it drastically.
In EToP, the manga tries to get it to seem more plausible in real life. Because there is a wide range of people who have seen the anime, it wants to get them to be interested in it as well.
PokeSupe wasn't intended to reach the same fans as it did as EToP. PokeSupe was intended to give the games a supposedly deeper plot and more characterization. While it is your opinion to say that the art is poor, it is far from that to say that about the characterization. Some of the characters of PokeSupe are given far more background than I've seen from EToP. I don't know how far you've read, but clearly it isn't enough to have seen the story behind Blue/Green and Silver. PokeSupe gives player characters with virtually no personality; Red, Blue, Crys, etc... something the readers can relate to.
I think everyone keeps getting a misinterpretation of that quote. I'm pretty sure that he's not saying, "That one has better characters and story," but, "That manga is closest to having world like I envisioned. The rules and interaction are what I pictured." What I mean by this is, if the Pokemon world were real, you wouldn't have Pokemon directly sent to a box. You could keep as many as you want, but to officially use in a battle, you can only have six. Or Pokemon are not resticted as they are in the games. They can move freely, use attacks out of turn and moves that should have been forgotten, etc. I think that Satoshi Tajiri's should have a big impact on whether a manga is a good interpretation of Pokemon. He is its creator after all. Whether you like it/prefer it is all up to you, though.
There is quite a bit of shipping in PokeSupe that you would probably be interested if you got into it. I love that RocketShipping had a "happy" ending in that manga. In PokeSupe, even though several ships seem obvious and lean towards canon, there is only one that is official, so if you don't like the seemingly canon ones, no hurt to your ship. (I pretty much ignore the ships since most of the "canon" ones are completly against I like because of the games)
EToP should have been longer. I'm really upset that they cut it short. I would have been interested in what it did with Ash and Misty and how he would have delt with May and Dawn's entrance.