I'm afraid that would be too much; that means I'd essentially have eight versions (four for HG, four for SS) and that's way too much effort to maintain. I do understand the purist viewpoint, but think of it this way; it's not actually that different! It just means the E4 challenge is cut out and moved; the way I intend to do it means it'll basically be the same as before. Instead of Eight Badges -> E4 -> Eight Badges, it'll be Eight Badges -> Eight Badges -> E4. Plus, the E4 has a more epic feeling that late, imo.
I understand your point of view, but something got in my mind after I thought about it. How do you plan to implement the actual travel of the character to Kanto? Because, for example, in the current version it's like in the original game, you go through Routes 26 and 27, then Victory Road, and when you beat the Elite Four you go to Vermilion by S.S. Aqua. If you make the character go to Kanto via Victory Road, I think the S.S. Aqua loses its point, and if you make him go via S.S. Aqua, then there's nothing to do in Routes 26 and 27 aside from that Tohjo Falls sidequest you introduced. Also, depending on what you choose to do, you'd have to again modify the order of the gyms in Kanto, so that you go in a similar way you do in FRLG, although it wouldn't be very difficult probably.
An idea you could do which would probably take less effort and achieve the same effect is to force the player to beat the Elite Four rematch to unlock Mt. Silver and all the other events which are normally unlocked after obtaining 16 badges. Right now there isn't much point in the E4 rematch (other than a challenge), and if you make it so that the player needs 16 badges to fight the E4 for the first time, even less so (unless you remove the rematch, but that wouldn't be nice! ). I think fighting the E4 twice for storyline purposes would be much cooler.
Also, is it possible to add trainers to the Victory Road? That would make it much better!