Setting such a low prestige threshold for an "active" player is downright worrisome. It's easy to get the first bit of prestige, regardless of when you start the round. Also, it's been proven in city competition after city competition and in Endgame after Endgame, the number of players actively hauling (or who would be if they were awake and online) is NOT necessarily the same as the number of connected players who have logged in within the past 72 hours.
I like a combination of suggestion by Hear Me Roar and Rhoswen, with an added tweak of my own.
What is "active" for Endgame purposes?
An "active" player should be one who has logged into the server within the past 24 hours (12h for x2) leading up to Endgame. Once EG starts, I'd reduce it to 12 hours (6h for x2) for future figures, but maybe that's just me.
Who should be factored in a Megacity's numbers?
Residents (home city) with at least 10,000 prestige (suggested by Hear Me Roar). It's not hard to get that much prestige if you've played a few eras, and if you haven't played a few eras then you won't be helpful enough to be considered in the requirements. The home city requirement prevents counting players who connected on their way to somewhere else, for pax runs, etc. It also prevents players connecting in during EG to purposefully drive up the numbers; new connections wouldn't be counted since they can't change home city.
What about prestige from hauling to a Megacity other than your home?
If NO prestige was offered (per Rhoswen's idea), you'd discourage sabotage even further. It'd still happen some, I'm sure, but it would undoubtedly be lessened. Keep the 5k bonus for being connected to the winning city. If all hauls to Megacities must generate prestige, then maybe decrease hauls to a Megacity that isn't your home city (give 1/2 or 1/4 value) -- that would allow those who weren't connected to a Megacity pre-EG to earn some of the prestige, also, while still discouraging active sabotage.
As it stands now, this change not only hurts cities with easy-to-reach locations that tend to attract more traffic, it also makes sabotage even easier than it already was. This isn't something that makes the game better, or more enjoyable, regardless of how it might affect the time it takes to complete the Endgame or seemingly "balance" it all for cities that don't have a larger group working together. This feels like a step in the wrong direction, but it's one that could still be framed into something that works better for us all.