IMO you are looking at it from the wrong way. You should not do comparisons. Just take a look at what exactly the size increase does. The character gains an effective +3 Atk, +6 Dmg, +lvl hit points, reach, -something on hide and the ability to use huge weapons and carry a lot more load. The dex decrease and natural armour increase are modified away against each other. It looks not too bad that way. Not too mention the difficulties for a large creature with wings to find armour that fits (magical armour does not automatically take the wings into account) and huge weapons will not be easy to find.
To be honest, I do not have Tomb and Blood at hand to check exactly what is written there. Somehow I feel the designers would have done a better job, if they just had desided the new half-dragon can now fly (no matter what size) and increase the spellcasting level 7 times (and made the HD d6). Or that they could have stated that the size increase would be similar to the MM but without the actual attribute and natural armour modifiers (basically gaining -1 atk, -1 AC, reach, ability to use huge weapons and all the downsides of being a large winged creature). The problem now is that they mention some things that change due to size increase, things that are natural part of a size increase, but do not not excluse anything spefically. To me it looks like they are given examples of what size increase will change. If they would have excluded bards from the prestige class and made a minimum spell level of 3 things would also have been different.
O well, I still think if you go for a size increase you should go all the way for logical consistancy.