The description of the 3rd-level spell sticks and stones [necro] (Shining South 49), in part, says
You animate a pile of rocks, branches, limbs, and other debris into the crude shape of a skeletal creature of Medium size that immediately attacks whatever foe you designate.… The creature’s combat statistics are those of a 2 HD humanoid skeleton, except that it also has a wight’s energy drain supernatural ability (see the Skeleton and Wight entries in the Monster Manual [225–7 and 255, respectively] for details). [Links mine]
With this in mind, here's how this DM would answer your questions:
"Can the caster have the skeletonlike creature use as the base creature any humanoid creature?"
Within the spell's limits, yes. The caster can pick to make the pile of debris emulate any creature that possesses both exactly 2 Hit Dice and the type humanoid (Monster Manual 310). My research shows that this means picking from gnoll (MM 130–1), lizardfolk (169), locathah (169–70), troglodyte (246), flind (Monster Manual III 62), phaerlock (Underdark 97), and quinametin (Dragon #317 65). These last two creatures are awesome, but gnoll is thematically appropriate as Shining South features gnolls prominently. (The region even includes the Gnollwatch Mountains!)
"Can the caster's skeletonlike possess ability scores of the caster's choosing?"
Not in this DM's traditional campaigns, no. In this DM's traditional campaigns, the caster will see the spell sticks and stones animate the debris as a skeletonlike creature that possesses the ability scores of a normal, boring base creature. The ramifications of ruling otherwise sends ripples throughout the rules that would require this DM to design a campaign that could accommodate that ruling.
To be clear, the game doesn't say that this can't be done, not saying that the caster can't have his skeletonlike animated pile of debris possess ability scores of his choosing. However, allowing the skeletonlike creature to possess arbitrarily high ability scores because the game isn't specific in this regard, by extrapolation, changes a traditional campaign fundamentally.
That is, the 1st-level Sor/Wiz spell summon monster I [conj] (Player's Handbook 285–6, 287) et al. and similar spells also have no such explicit restrictions against picking the ability scores of the creatures they bring forth. And bringing forth, for example, a celestial hawk that possesses Int 3 yet each other ability 9,000—even for 1 round—for but 15 gp (the price of 1 charge of a wand of summon monster I) is something that warrants a specific campaign.
"Could the caster animate the debris so that the skeletonlike creature possesses a template?
Again, not in this DM's traditional campaigns. In this DM's traditional campaigns, the caster will see the spell sticks and stones animate the debris as a skeletonlike creature that was originally a 2-Hit Dice humanoid creature that now possesses only and exclusively the template skeleton. (Even then, remember, it's not a real skeleton but an ersatz skeletonlike creature and, in actuality, a magically animated pile of debris .) As with ability score improvements, the ramifications of ruling otherwise sends ripples throughout the rules that would require this DM to design a campaign that could accommodate that ruling.
Again, though, to be clear, the game doesn't say that this can't be done, not saying that the caster can't declare that his skeletonlike creature possesses an arbitrary number of appropriate templates so long as the skeletonlike creature retains its type and Hit Dice. However, allowing the skeletonlike creature to possess an arbitrarily number of templates because the game isn't specific in this regard, by extrapolation, changes a traditional campaign to the core, so this DM would say no again unless the campaign were designed to deal with this eventuality.
For example, were a caster allowed to, by extension, employ a positive ruling in this regard in conjunction with the 1st-level Drd spell summon nature's ally I (PH 288), the caster could bring forth a dire rat (64) or a fiendish dire rat (MM 107–8) or a dire rat to which has been applied the templates half-dragon (MM 146–7), half-fiend (147–9), and even paragon (Epic Level Handbook 208–10). (Also see this similar question for Pathfinder.) Again, were it possible in this DM's campaign to bring forth or create creatures that possess an arbitrary number of templates, that would be something to design the campaign around.
Note: This player can totally see where you're going with this. The sticks and stones spell kind of sucks if it can't be tricked out in the ways the question would like, despite it being pretty much the earliest spell a caster can use to get to an energy drain effect. However, the idea that the rules don't say you can't isn't usually justification enough for this DM to rule in favor of utterly broken readings like arbitrarily high ability scores or an arbitrary number of templates. Such rulings necessitate their own dedicated campaign.