MacGyver/The Doctor

[Phelix-Mu]

Thing is, The Doctor, as awesome as he is, has no real powers outside of the Screwdriver, the Tardis, the psychic paper, Regeneration/reincarnation and massive intellect. Regeneration can be granted by a template, race or magic item; the paper, Screwdriver and Tardis are obviously magic items or artifacts. That leaves the intellect, which Expert emulates just fine.

Actually, you've overlooked quite a lot. Even focusing on the new doctor, he's shown to have some strange ability to redirect energy that he absorbs, as well as having some kind of racial energy resistance . Ability to metabolize poisons also came up in that episode with Agatha Christie.

The old doctor used powerful hypnosis on numerous occasions. Low-level telepathy. Ability to meditatively slow and virtually stop his metabolic functions. Ability to stop both of his hearts (feign death). Ability to stop breathing for prolonged periods of time. One of his regenerations had access to some pretty extreme barehanded combat ability, and it's later implied that he could still use it, just that the personalities of his later bodies all had an even greater distaste for violence. He should also have crossbow proficiency, possibly also bow proficiency, and mad fencing skills. He knows a lot about combat, just he intentionally never uses it.

Now, as I said before, actually modeling everything that he is capable of doing is quite hard. Skills-based should be the go-to flavor, since the Doctor pretty much laughs at AMF. He is way, way more dependent on his screwdriver in the new show. It was around a lot before, but even without it he routinely escapes bonds, picks locks, bypasses security systems, and such. The screwdriver is a great asset, but it's hardly a crutch. He also had a sonic lance at one point, like a screwdriver but more focused on building things than taking them apart, as far as I could tell.