1:Yes. Basically any template that isn't MS Word is acceptable. If you use one available on APC or another template website, you're still ahead of the MS crowd. What I recommend is looking at various templates and choosing one that fits best, and then modifying it to fit your particular resume better. No two resumes are the same, so why use the same template?

2:SOME airlines accept resumes online, not all of them. Regardless, while some airlines certainly utilize www.airlineapps.com, not even all of those are exclusive to those. Airlines will always request a resume after reviewing an application online. It never hurts to send in a solid cover letter that is unique and has unique points about the airline (not "XXX is an industry leader, I wanna work there, great place to work, etc) along with a resume. If you're somebody screening resumes and you get a nice little packet from somebody that is well written, interesting, and concise, wouldn't you bring that person in over one of the hundreds of people using airlineapps?

3:Eh. Sure. Yes and no. Sort of for the reasons I mentioned above CVs are a little different from other industries. CVs in general always have the same purpose: to get your experience across enough to get an interview. In aviation, that happens to be a little bit more straight forward and, unfortunately, arbitrary. Because of the vast amounts of pilots out there, and the relatively dull seniority system, it pays to keep your resume concise and highlighting certain distinctions you've received. A pilot that flew for a legacy for 20 years certainly has a lot of prestige, right? Well, all that pilot can say for their title is "Captain", and any person who reads that knows exactly what that is, and will sift through any BS. That title, unfortunately, is the same title as a 4 month employee of Mesaba. For that reason, titles and jobs necessarily speak for themselves in aviation, and because of this, a resume is that much shorter. No BS. And that's why I say unless you're applying for something other than a purely flying position, all that really matters is your flying jobs, any awards you've gotten for them, your flight time, any military time (ANY, not just recent or active duty) and the institution where you got your degree from (if you have one). With all that, even if you've had multiple flying jobs in the past, you'll be hard pressed to fill up more than a page unless you start yanking around the resume reader with terms like "To use my excellent piloting skills to yada yada yada".

Remember. KISS but show that you're different.