Wow, we could talk a lot about what we feel affects this. It has been shown empirically that if you add plenum to an intake and dyno the car, it will make more power by adding plenum. Problem is, once you reach an "optimal" point on plenum size for the particular combination of parts you have, the shift recovery suffers. Why is that? In my opinion, the plenum and to some extent an increase in runner section act has a shock absorber or air capacitor. If you have too little or too much the results will not be optimal. The plenum acts as an incoming air reservoir for the runners to pull on. If it's too small, the runners compete for the same plenum air (If the plenum cannot supply the air, it must be supplied from the inlet and TB runner which takes more time and makes filling the cylinder more sluggish) and if it's too large and the runner section is also larger, the piston's affect on getting the air mass started is diminished depending on the rpm (depression or air mass movement of the pistons with respect to time so the air column can get lazy at certain piston speeds and that also depends on the drive train gear ratios) - we go from higher vacuum at lower piston speeds/small throttle angles to lower vacuum/open throttle angles but we move more air mass as piston speed increases.
Sticks tend to like larger plenums and automatics tend to like smaller plenums. There are no cut and dried rules in any of this - it's been learned mostly by experimentation by myself and others who write about it and varies with the combination of parts used.
In a power shift situation, the throttle blade has "minimal" affect on flow characteristics and harmonics. If you start using the throttle and not power shifting, you set up a new dynamic inside the plenum and runners, so shift recovery is dependant on other factors too.