I cant believe I missed this article. I currently run a Raichu deck except my deck was quite a bit older. I had 4 Shaymin EX, Hawlucha FFI, and a few other small things like Repeat Ball. I was looking to update my list though. I wasnt sure which type to swap out for Hawlucha and it looks like Yveltal or Milotic is the way to go. In addition I switched two Shaymin EX for a 2-2 Octillery line (cause Im poor) but it looks like I'll have to switch to 3. Finally you convinced me to go find a promo Jirachi.
I think the fighting variant you mentioned is interesting. There is a reason why I did choose to play Regirock in my version and it's because it can hit for weakness unlike Hawlucha. I know many times you are off by like 20-80 damage and Hawlucha can do that, but it needs to be an EX for that to even work. Regirock can hit for 60 regardless (but with 2 energy) and 120 if it's an EX (or 240 if weak to electric).
As for the octillery, I think it is an OK substitute, but what I see as a better alternate is Unown AOR. It can sit on the bench for 20+ damage on Raichu or after a bad Judge/Birch it can be 1 more card. I personally would go with the Shaymin-EX if you owned any, but as a 2nd choice I would try to fit in 4 Unown (and possibly a line for Octillery as well, but the list would be tight).
And Jirachi is great. It has won me many games and definitely changes your opponent's strategy if they see it come down.
Question though, you said the M Manectric matchup is in the Raichu players favor, but the way you describe it, it sounds more like its in the Manectric players favor. In my experience getting a full bench sometimes can be a little more difficult in the late game.
Another question is what do you think about the addition of Jolteon EX from Generations?
I'm not sure how I originally described it, but I'll try to fix the explanation below. First off, it depends which M Manectric deck you are playing. If you are playing against MMan/Water, you should have a better chance of winning. This is because Regice is not likely to KO you (lack of muscle bands in the deck and FF belt doesn't one shot you) and Articuno is hard to set up. It is easy to hit the 170 number on Manectric and possible with Bats to hit 210. If you KO a Manectric EX, all you really need to do then is KO 2 Shaymin-EX, which is very possible. A problem could be from stadium wars, but you should be fine as long as you play them down strategically and have ways to draw into a Shaymin as well.
The other Manectric deck is much harder, with Raikou. Essentially, with an assault vest, it's a 1 prize EX that one shots you with 3 energy. If I were to update this deck today I would definitely add either a Xerosic or Megaphone as that deck is somewhat problematic for Raichu. I will say that I do tend to draw better than those players, but I honestly haven't tested it with BreakPoint. I assume it would be good if not better, so that's why I think you would want to add a tool discarding card.
Lastly, about the Jolteon, I think it is interesting. Being able to stop basics from attacking is amazing. But the problem is that I do not think it fits into this deck. It needs 2 energy and is an EX, which kind of undermines the mostly 1-prize value of the Raichu variant. Once an opponent sees it go down on the field, I guarantee you they will aim for Jolteon right away. Granted, I have not tried it out and might try it now that you suggested it. I do think it makes Raichu stronger though. With muscle band on the low, Jolteon is hitting for 80, just shy of a Raichu KO, which is awesome if your opponent plans to centralize their deck on Jolteon.
