One can't have more than a single Focus.
But what of Tremere with Mythic Blood? Especially as there are (IIRC) 2 new mythic bloods in the tremere section on HoH:TL
I can't give you any way to reconcile the mythic blood and the Tremere bonus virtue.
However I certainly used to have a house rule that allowed Tremere to have a second magical focus (since then I've decided to change the Tremere virtue. It's easy enough to do when you're not running a game, more difficult to pull off mid-saga). I believe that I was not alone in having a house rule like this, in fact I thought this was fairly common.
I'd be inclined to take the effects of "Focus: Certamen" and rebadge it as a separate virtue. I don't see the danger in that.
I assume that the focus would (always) be "certamen", so the Tremere in question would just get the other Mythic Blood benefits.
Why not make Certamen an accelerated ability (or just a normal Arcane one if you prefer) and migrate mmf:certamen to Puissant(ability) Certamen or Affinity with...?
Seems to me it would maintain the spirit of the RAW whilst allowing for other schools of focus in Tremere like other Houses have.
IMO that is far too narrow a view. Since mmf:certamen is a House freebie, it would seem only just to allow one to BUY a replacement mmf (or equally one offered by spending 3 for Mythic Blood) to supercede it.
As already mentioned though, it seems to me that some revision of Tremere character virtues/abilities could only enhance the desirability of the House for many (not me personally since I can't stand Tremere or their hypocritical militaristic arrogance). Making such things as Certamen into a puissant ability rather than a focus.
Every SG has his/her own ways though. Just food for thought.
I don't belive making Certamen into an Accelerated Ability would solve anything. This would make it (back) into another thing to sink exp into. Even if the accelerated bit makes it in the same range as the Arts.
Having it as a Focus lets the Tremere master it, while not sacrificing any magical ability (arts). Just make it into a "special Focus" only allowing it for Tremeres, and having it mean, that another (normal) Focus may be purchased also.
In my campaign I rule that you can take any Minor Magical Focus in addition to Mythic Blood, since the Magical Focus in that virtue is a part of a bigger virtue. So I have no trouble with two Minor Magical Focuses in that instance. 
E.
We have always run the Tremere Certamen virture as "Pussiant Certamen" when the Tremere duelist receives a +3 to the strongest virture they use
That's a pretty good idea, actually!!!! 