In any fight where your Sceptile's grass attacks are doing super effective damage (which is where you'd be using it in the first place), bullet seed will outperform fury cutter due to SE damage and STAB. That said, fury cutter has crazy high EPS and is very easy to dodge with, potentially allowing you to get off another 1-2 leaf blades.
My opinion: Bullet Seed, if you're comfortable dodging with it, as it is a bit slower and clunkier but does higher DPS. Fury Cutter, if you're finding that you're dodging more reliably and able to get off an extra charge move or two that you wouldn't have gotten with Bullet Seed.
As for Meganium, unless you have a stockpile of TMs and no other viable candidates needing a move change, I wouldn't spend the TM on it. It's stats are pretty abysmal, so you're unlikely to ever use it.