Focus on story or servant

Assuming by story you mean the Singularities, I would say it's best that you don't focus on either.

While progressing through the story will reward you with Friend Points and Saint Quartz, you won't be getting enough Experience Cards from the Friend Point Gacha to reliably keep your Servants at a good level. If you focus on farming Embers for Experience Cards, you'll probably be leveling relatively underpowered Servants that get outranked as you go on, meaning you're wasting your time to some extent.

What I'd recommend doing is leveling your Servants to the point that the story isn't too hard and then go through story until it starts getting hard again. At that point, return to leveling your Servants until they're up to par and continue on.

If by Story you meant the Fate/Acel Zero event currently going on, absolutely focus on that. The QP, Asencion Materials, 5 Star CE, and 4 Star Servant you can get from going through it will absolutely be needed later down the road, and the event won't get a rerun for over two years, if it ever gets one at all.

Unrelated to the question but one thing I would recommend is keeping any Servants you can get from the Friend Point Gacha. Fuse them go get their Noble Phantasm level up to 5 and then, and only then, use them as a source of experience.

well, the challenge in the story will get harder as you progress especially after okeanos chapter, so it's best to upgrade your servant first

Leveling your servants would be wiser and for that, events should be prioritized as they are limited in time, give you the chance to get many materials for ascension/skill up, EXP cards, Fous, CEs or even very unique items like grails and crystallized lore. For example, the last event (Davinci's) allowed me to level up Jalter from lvl 1 to 90 very quickly.

Story are always here and sometimes, they do a 1/2 AP campain to clear it at half the cost of AP.