While it is not a top tier Mega, between the two it seems to fit better. For Water types, you already have a huge wall in the form of Toxapex, and M-Sceptile can still OHKO plenty with its Grass moves. The con is that you will have a serious Ice weakness (3 weak, 2 of which are 4x) where as with Manectric, you will have a major Ground Weakness (4 weak, all 2x). While this Ground weakness is somewhat remedied by Togekiss, it alone does not have enough firepower to easily KO most Ground threats, or faster sweepers with EQ. Further, a lot of EQ users also have Stone Edge/Rock Slide which is again something you don't want your Togekiss to go against.
Further, M-Sceptile also boasts of a more diverse movepool, with Grass (Leaf Storm and Giga Drain) and Dragon moves at disposal as well as EQ, X Scissor and so on. In comparison, M-Manectric is Overheat + Electric STAB move, and little else for effective use.
A typical moveset for M-Sceptile used is a mixed set, with Leaf Storm, Drain Punch, Earthquake and Dragon Pulse, although you can mix around based on team requirements. Alternatively, a pure Special Attacker in the form of Dragon Pulse, Focus Blast, Giga Drain, Leaf Storm/HP [Fire]/ EQ also works well.
Other uses for M-Sceptile are to stop VoltTurn teams with Lightning Rod or as a Physical Sweeper with Swords Dance.