IMO, the worst offender of stand-up regeneration making no sense was when Mels regenerated into River in Let's Kill Hitler. After being shot, she was laying on the ground bleeding to death, and then when she started glowing from the regeneration energy, she instantly stands to assume the position.
IIRC, RTD intentionally wanted Eccleston to stand for his regeneration specifically because it was different from all the previous regenerations. Ironically, all regenerations since with one exception have copied this.