The cups and balls routine I perform is always done standing up, so that is all I can speak to. IMHO, a routine with final loads, if done smoothly and deceptively, will always surpass one with no final loads, that is to say in terms of LAYMEN impact and reaction (different rules apply for what impresses magicians).
I have always used 4 final loads, with each being of a different bright color because I feel it results in essence in 4 separate effects, whereas I believe uniformity/identicality of the final loads (e.g 4 yellow tennis balls, 4 white baseballs or 4 lemons), while still very strong, dilutes the impact. I have also found from experience that fruit elicits a substantially stronger reaction than big balls. My current final loads for C & B are a lime, an orange, a red potato and a lemon. All I know is it kills! I think the sheer incongruity of fruit exponentiates the surprise and magical effect.
Additionally, I do not consider loading from the pockets a liability or weakness. I have literally never had a layman say "those balls must have been in your pocket," nor (at least to my knowledge) have I ever been caught in the last 20 years in the final loading sequence. If the timing is right, the misdirection is perfect. I like to propel the little ball forward a bit when I lift the cup for each final load (an idea certainly not my innovation), as their eyes have to follow the movement, and it adds an extra compelling layer of misdirection. Again, just my opinion.
BTW, I recently sprang for a set of the Brett Sherwood nickel plated cups and 2 sets of his custom made balls in royal blue. If I could marry a set of cups...
Also found myself unable to resist ordering a custom wand from Allivan to go with the new cups. (Ebony with Purpleheart tips - beautiful piece of art!)