So are there others out there that think it can be hard to create a character without getting some aptitudes they don't think belong with the character?

I am thinking on allowing my players to change one aptitude to another of their choice after selecting a role and dealing with duplicate aptitudes, as long as they keep the professional (non-characteristic) aptitudes to a maximum of three.

I have not done any character creation yet, so what are the experiences of other groups out there?

Does a free selection of 4 characteristic and 3 professional works better?

I think it can be.

And I hate, hate, hate apitudes with the righteous flame I normally reserve for the Xenos. Most likely apitudes are the visible signs of Eldar intrigues within the Imperium.

I'm still sticking to my OW way of doing this; after creation but before expending experience, each character is allowed to switch out one Professional Aptitude (Knowledge, Fieldcraft, etc) and one Characteristics Aptitude (Toughness, Willpower, etc) for a corresponding Aptitude each.

This does not include "special" Aptitudes (such as Psyker or a theoretical Navigator Aptitude).

Chirurgeon seems to be the most egregious offender (it's easy to make a character in this role without needing Strength), but switching out one aptitude for another from the same category when it makes sense for the character is a reasonable change IMHO.