@symptomz: Hm yeah, I can see the problem. I would just follow the "National Dex" order but put in the extra evolutions/pre-evolutions before or after where their original forms are, the numbering will look weird but whatever.
The other options would be to either wait until all new evolutions are added before making a tree, which in some cases would take a looong time (prime example: Eevee), or just keep them as separate entries once you add them and not include, for example, Politoed in the Poliwag tree.
Man, thinking about it, is there even a single Generation 1 pokemon that only had one form that hasn't had another added by now? Ok so there's Lapras...and Pinsir, but you get the idea.
Edit: Oh yeah I forgot, but that Pidgey looks more badass than any Pidgey has any right to do.