I don't think there are that many things Klentak can do differently at this point.
1) Aren't a lot of Cubans left, and they're no longer bargains
2) You can trade for LA allocations, IF someone is willing to make a deal at a reasonable price
3) He's shown he can move money up and down the amateur draft.
As far as trades, Phillies don't have much of value right now, you don't sell low by trading prospects, you have to get them to the majors and increase their value, which is why I don't fret about Rupp, if he didn't improve, he didn't have that much value last year, the downside to these guys isn't low unitl they become 3-4 WAR players like Hernandez (teams don't trade blue chip prospects for 1 WAR starters). Yes, they'll get something for Kendrick, Neshak, Nava, Hellickson (if he keeps pitching well), but nothing exciting.
Sometimes you're constrained by reality - at this point all they can do is patiently wait for prospects to arrive - this winter they have to make a tough decision between Hoskins and Joseph (he's not moving to 3B, isn't quick enough), but the OFs are a year or two away from trade bait - no one is breaking the bank for Cozens until he show he can hit the curve on a regular basis. And so on. If Kingery is ready, Hernandez is a possibliity if he comes back healthy.
There just isn't much they can do other than just keep adding talent.
Better coaches will help, but usually you have to be already on the upswing before you can hire them, because if they're good, they have other opportunities.
Free agency is a couple years away, you don't overpay for mercenaries, you wait untl the team is good enough that its attractive to the kind of FA that will be a good fit on and off the field.