The Pats have a bad record in Denver because in many of the games played there they were by far the inferior team. Let's consider the Belichick/Brady era: In 2001, the Pats lost an October game in Denver. That was a Patriots team that was still finding itself. It was also Brady's 5th career start, and he threw 5 picks.
In 2003, an outstanding Patriots team beat a solid Denver team fair and square.
In 2005, the Pats defense had slipped mightily from their perch the prior year, and a vastly superior Denver team justifiably beat NWE twice, once in the playoffs.
The 2009 Adalius Thomas led Patriots remain by far my least favorite team of the entire Belichick/Brady era, and that team's performance has no bearing whatsoever on any potential upcoming playoff matchup in 2016.
The Patriots crushed the Tebow's in 2011.
The 2013 Pats didn't have Gronk, Amendola was hurting, and lost their only reliable corner early in the game. And that Denver team was actually, you know, pretty good.
The 2015 game has been discussed and dissected. It's one of those "what if" games that sometimes happens.
As for the acclimation, I seem to recall reading somewhere that there is some benefit to getting out there a couple of days early, and I wouldn't be surprised if the Pats did go out on Friday for a Sunday game (or Thursday for a Saturday game). However, to completely acclimate would take a matter of weeks, not days, so there's not much more visiting teams can do to combat Denver's climate.