Climb-speed, swim-speed, burrow-speed?
I'd pick the last one.
Did he go into this ritual knowing what he was getting?
If so, then I'd say tough tassels. He wants to lose the wings, here's a red hot longsword, go to town. :)That will that give him a huge RP character storyline for his biograpny, and since he's got the buttload of overpowering from the template, you could even reign in some of his bonuses that might be legitimately tied to that action.
alertness and blind-fight as bonus feats perhaps, it would represent his enhanced senses.
Looking up green dragon I see :
Wyrmling, waterbreathing and a swim speed
Very Young, woodland stride
Young, entangle 1/day
Juvenile, frightful presence, charm person 1/day
These abilities seem most suitable to replace other abilities, in the case of losing wings. waterbreathing and a swim speed seem most appropriate though less often useful adding woodland stride seems a fair deal in my opinion.
I'd add a tail and webbed claws to justify the swim speed but I am not sure your player would like that any better (I do though).
I need something cool, interesting or useful to replace half-dragons wings with. My player just became a half-green dragon through a ritual, but he doesn't like the wings. That's why I'm trying to come up with an ability or a bonus worth more-or-less the same as the wings, because I don't want him to lose on power.
A Tail lash as an additional natural attack?
dragonsking cape (like wings that don't function), you gain evasion against that particular element. Example fire: you get evasion against fireball, but not cone of cold.
Breath Weapons are cool. Give him 1d6 per character level 1-2 times per day.