2. Nearly everyone other than Trump supporters expected Hillary to win. Why would the Russians back a losing candidate?
3. The Russians had spent years buying off the Clintons and their supporters. John Podesta was bought and paid for. Why would they through all that time and investment away?
The only explanation is that the Russians were simply hedging their bets. They wanted to have some contacts in the Trump camp on the off chance that Clinton crashed and burned.
The Russians want NATO off their borders just as we would want the Warsaw Pact out of Mexico and Canada. It is an understandable instinct of self defense by Moscow.
“I cannot forecast to you the action of Russia. It is a riddle wrapped in a mystery inside an enigma; but perhaps there is a key. That key is Russian national interest.” - Winston Churchill
There are at least four completely independent things; possibilities, suppositions.
1: Russian non-gov’t actors may have attempted to influence US elections as an act of “vandalism”.
1A: They may have tried to do so via the release of embarrassing HRC emails which she embarrassingly left out for literally anyone to grab. It’s likely, IMO, they succeeded.
1B: They may have tried to actually bust into election tallying mechanisms. I think their influence here is/was minimal if not nonexistent.
2:2A:2B: Same as above, the Russian government.
3: Trump or his campaign may have colluded or sought advantage with either of the above. IMO this did not happen and not even close.
4: DNC insiders resentful of the treatment of Bernie may have leaked internal emails. I think this is likely, indeed, the most likely.
The Trump collusion angle is simply the least likely and IMO flat out did not happen, and there is zero evidence that it happened.
the russians are our natural allies.

Unlikely on both counts. Donald Trump talked about making NATO countries pay their own way. That doesn't look like a US build-up of forces in Europe. Talk about "America First" likewise suggested that we weren't going to increase our forces overseas.
Defense spending did decline under Obama, but was that because troops and weapons were cut or because we withdrew from some conflicts? I don't know, but Hillary is more hawkish than Obama was, and she wouldn't simply continue his policies on defense and the military. Do you really see the woman who wanted to intervene in Syria increasing welfare at the expense of the military?
Therefore, given the two bad possibilities, the Russians would prefer Hillary.
The theory is that the Russians just wanted to throw the US and its alliances into chaos and electing Trump would do that. Plus, HRC supported sanctions on Russia, and the Russians may have thought they'd have a better chance with DJT. I don't think the Russians "hacked the election" or that Putin loves Trump, but the idea that they had a natural preference for Clinton doesn't hold up.
“Therefore, given the two bad possibilities, the Russians would prefer Hillary.”
I disagree. The Russians, correctly, regard Hillary Rot-ham as deranged, unstable and malevolent. They think that she would force a hot war through her incompetence and ignorance. Initially, they thought they could reach some rational equilibrium with Trump, in sort of a Detente, second edition process. They are doubtful now, given the neocon bleatings and squirmings of late. A number of Trump supporters are doubtful as well.