It's hard to express how relieved I am that we are hiring Towers rather than going with a cheaper DiPoto. I still don't believe getting rid of Josh Byrnes was the right decision, and it may yet haunt us. However, Towers should be decent, and I simply just don't trust DiPoto yet. Part of this is due to the statements he publicly made about Joe Saunders and wins. While that may be just an excuse or reason for him to throw at the public, it's still disheartening because you simply don't see other "good" GM's making similar statements. I still don't like the Haren trade, and think the trigger was pulled prematurely. As for the Hudson trade, I applaud him for pulling the trigger, but I don't really think he should be rewarded for a trade that any reasonable GM could have done, given how eager the White Sox appeared to be shopping Hudson/shopping for Edwin Jackson.
Still, these are just opinions, and it would be useful to look at Kevin Towers's actual history with the Padres to get a better idea of what we can expect. All information comes from MLBTradeRumors's feature that provides GM histories. I only looked at recent years, as going back further is made much more difficult by the fact that I only started following baseball recently.
With regard to trades, Towers appears to be pretty solid. The most famous deal he made was probably the one which brought Adrian Gonzalez and Chris Young to the Padres for next to nothing. However, from what i gather, a lot of people think he got lucky on that trade, as Gonzalez had sucked quite a bit in extended time in the majors during the two previous years. Aside from that, he's never made any big, flashy, blockbuster moves that I can recognize, which depending on your point of view, could be either a good or bad thing. He has definitely made many solid small moves, trading away pretty useless pieces for very useful bullpen pieces. The current manifestation of the amazing bullpen in SD is almost entirely due to Towers's trading, as he obtained Heath Bell, Mike Adams, Luke Gregerson, Joe Thatcher, Ryan Webb all for next to nothing (though admittedly a couple of the pieces he traded away could have been better than they turned out: Khalil Greene, Brian Sikorski, Scott Linebrink). The big thing that stands out though for me, is that he hasn't made any colossal errors. I honestly feel this is perhaps the best criteria with which to judge GM decisions. I feel like that's much more important than most people realize. Towers even managed to trade away an expensive, overrated, injured pitcher (Jake Peavy) to the White Sox (I see a pattern here...) for a solid four pitcher return that includes Clayton Richard (a #3 starter based on that BotB article relating WAR to starting pitching numbers), Adam Russell, and Aaron Poreda.
Perhaps the most impressive aspect of Towers is his ability to get cheap initial signings/extensions. In the past decade, he's managed to obtain Ryan Kiesko for 3 years/$18.75 million in 2000, Jake Peavy for 4 years/$14.5 million in 2005, Chris Young for 4 years/$14.5 million in 2007, Adrian Gonzalez for 4 years/$9.5 million in 2007. The problem is, after these initial signings, Towers seems to then hand out slightly overpriced massive contracts. While I do feel that a lot of these overpriced (albeit only slightly) were not foreseeable, it does worry me. Kiesko was given a 26.5 million three year extension after three initial years of around 4 WAR, only to see his production drop to around 1.5 WAR per year after the contract. Peavy was given a hefty 3 year $52 million extension in 2007, and he has also fallen short of this contract, though Towers did manage to trade Peavy away. Maddux had an unwarranted expensive resigning, and Towers also signed Trevor Hoffman to a couple of expensive contracts, in which Hoffman underperformed. However, Towers's trades in recent years suggests a changing stance, showing he believes trading for relievers may be a cheaper and more effective method towards building a bullpen than via free agency and signings.
In my mind, this is probably Towers's greatest weakness. Beyond the Box Score ranked the Padres's farm system right in the middle, 15th out of all teams in the major leagues. Not bad, but by no means stellar. A look at Towers's "notable draft picks" of the past decade and the land is really barren. Yes, he did draft Mat Latos. But only being able to draft one ace over the course of ten years and a couple hundred rounds is worrisome. Recently, there's been some optimism, as much like the Dbacks, the talent in the Padres's farm lies in the low minors. Still, there just hasn't been enough impact players coming out of Tower-led drafts. Through a combination of emptying via trades, graduating to the majors, and the departure of Mike Rizzo, the Dbacks farm has been consistently ranked among the worst the past couple of years. I'm not convinced yet that Towers will be able to make this portion of our front office better.