Choice Specs is better
This holds true in general, and is definitely the case in NU, which is where Magmortar usually resides. The reasons for this:
- The greatest difficulty Magmortar faces are bulky Rock and Water types, which are usually very slow so Magmortar does not need the extra Speed that a Scarf set provides, but it does convert some 3HKOes to 2HKOes after hazard damage with Fire Blast or Focus Blast:
- [Rhydon is 2HKOed by Fire Blast with Specs, so it can't switch in, whereas with Scarf, that becomes a 3HKO and Rhydon can use EQ. Note that Rhydon's fastest typical set is still slower than Magmortar with 116 EVs invested]
[252 HP Vaporeon has a very high chance (99%) to be 2HKOed by Focus Blast with Specs after Stealth Rock damage, so it can't switch in, whereas with Scarf, that becomes a 80% chance to 3HKO and Vaporeon can use Scald. Note that Vaporeon's fastest typical set is still slower than Magmortar with 116 EVs invested]
Magmortar is not very fast to begin with, so it is easily revenge killed by faster Scarf sets and other fast Pokemon in general. Since it has a poor defensive typing and is susceptible to hazard damage and other passive damage, it can be KOed by priority.
- Magmortar is typically used as a Wallbreaker, and Scarf greatly takes away from that role. If you need speed control, then it's a task best left for other team members. In that regard, having Sticky Web set up is essentially the same as Mag having a Scarf, and it helps other team members too, so that's a good workaround for speed. Of course it's a little trickier to keep Webs, but the benefits should typically outweigh the risks, at least versus underprepared opponents limited or no hazard control.
- The best sets are the Firium/Fightium Z sets because they can take down otherwise troublesome walls, followed by Specs. If you have other strong(er) Pokemon to handle those, then maybe, just maybe you can dedicate the Scarf slot to Mag, but even so there are many other Pokemon which are better suited.
Do note that these observations are made based on the NU usage, but the power creep as you rise above towards OU only means that Magmortar's subpar base 83 Speed and its lack of 252 Speed EVs and no boosting nature only becomes that much more relevant and makes it less likely to be effective unless you achieve a very specific set of win conditions. Finally, a disclaimer: This answer does not take into account your other Pokemon and your playstyle, so while this holds in theory, your mileage may vary in practice.
