Actually, that's exactly what the word 'reboot' means. To start over. That's why DmC has a totally different plot, with Dante not getting a Devil May Cry demon hunting agency, with a city called Limbo, with different... everything.
I suppose they could just fix the important things, but then, you'd still be stuck with 'Wesker had a son, who's already in his twenties or something' and of course the fact that Leon is now a very serious guy, unlike the one in RE4. They have to find some way to fix it all.