You know, I ran a little test to see how it would pan out over the career and I was a little surprised in what I found.
Taking a Human to start with and progressing him along the route of:
Fighter 1, Sorceror 1, Fighter 3-5, DD 6-10, Fighter 11-15, DD 16-20.
HP 114
Fort +13, Reflex +6, Will +12
BAB (including Str Bonuses and size mods) +19
13 Feats
+4 Nat AC, but a -1 AC due to size too.
5x cantrips, 10x 1st level spells (not including cha bonus)
Str 18, Dex 10, Con 12, Int 12, Wis 10, Cha 12
Taking a Human Half-Dragon
Fighter 1, Sorceror 1, Fighter 3-18 (ECL of 20)
HP 139
Fort +11, Reflex+5, Will +7
BAB (including Str Bonuses, no size mod cos medium sized) +20
15 Feats (I included the bonus feat for humans here)
+4 Nat AC
5x cantrips, 3x 1st lvl spells (not including cha bonus)
Str 18, Dex 10, Con 12, Int 12, Wis 10, Cha 12
So, it's fairly east to spot that, if you take the extra feats the half-dragon has and put them into +2 fort and will saves you are still down on what the DD has, although the DD has lower hps it has the benefit of wings (which the half-dragon human does not have as it's size stays Medium).
Even without the stat bonuses for a size increase, it seems that the human dragon disciple has definite advantages over it's half-dragon cousin and giving it stats for a size increase would probably tip the balance MUCH in the favour of the DD.
As well as this, the DD has definite HP advantages in the early levels which is sure to help out, and it's only when the DD actually starts transforming that the half-dragon catches up.
The only thing I forgot to mention in all this is the fact that the half dragon also has it's immunities, extra stats, extra AC and breath weapon straight from the start, unlike the DD who has to wait all the way to the end for them.
Given this comparison, what do you guys think? I used the straight fighter comparison for the dragon disciple/half-dragon because it made most sense. I haven't counted for any wierd combinations that could be made out of it all.