“There’d be a ton of reasons” why Charter Communications “would likely pursue” the No. 2 cable operator if federal officials nix Comcast’s $45 billion stock deal to buy Time Warner Cable, Liberty Media CEO Greg Maffei told investors today at Morgan Stanley’s Technology, Media & Telecom Conference. He should know: Liberty, which is controlled by chairman John Malone, is Charter’s dominant shareholder. The cable company tried to buy Time Warner Cable last year, before it was outbid by Comcast.

Charter’s in a better position to act now, Maffei says. It can more easily afford a deal: Charter’s stock is up 47.5% over the last 12 months while TWC is up 11.7%. Maffei also talked up Charter’s management under CEO Tom Rutledge. The Charter chief spoke at the confab earlier in the day and said that he’s pleased with a deal he made with Comcast — if its deal with TWC closes — that would enable Rutledge to pick up many of its subscribers, and swap others.

Malone has made no secret of his lust to make another run at TWC. Asked in November whether it would be a good idea, the famously plain-spoken exec said, “Hell, yes.”

Comcast Time Warner CableComcast CFO Michael Angelakis told the investor gathering that he expects the regulatory process to wrap up “shortly.” Meanwhile, “our teams have spent last year working on integration. We have literally hundreds of people working on the integration which is relatively complex, but I think we are really excited that this will be a great transaction for the company.”

Most analysts still think that Comcast will prevail, but are less confident than they were last year. A few weeks ago MoffettNathanson Research’s Craig Moffett dropped his odds of success to 60% from 70%. And yesterday Needham & Co analyst Laura Martin dropped her assessment of TWC to “underperform.” If a deal falls through then Charter’s offer would be “lower than its last bid of $130/share.” She attributes that in part to the FCC’s recent net neutrality rules “coupled with the fact that we would expect no competitors in a next bid from Charter.”

Rutledge, for his part, says that the FCC decision to regulate broadband as a public utility “has raised the level of uncertainty” — adding that Charter “will be involved in the litigation strategy and the legislative strategy as well” to see if Congress can overturn the ruling. But he added that if the FCC holds true to its word to not regulate rates then “we should proceed as we expected to proceed. And that’s what were doing.”

Maffai says that Charter will be fine no matter what happens with Comcast and TWC. If they combine, then it “is likely to be out of the market as an acquirer of incremental U.S. broadband and we will be the company with the highest number of synergies to bring to bear.”