I wonder what the effects budget is. Skimping in that area could be detrimental to the show, though I expect that Disney/Marvel have enough in-house expertise to make it look good.
Other shows sometimes haven't fared very well in this area. NBC slashed the budgets on Heroes to the bone, which resulted in the writers/producers having to cut major sequences and alter plots. The season one finale had most of the planned effects sequences cut, which severely impacted the episode. I'd hate to see SHIELD get short shrift like that.
I'm not too concerned about the FX. I think what is important to remember is that this show will probably feature smaller, street-level heroes and villains. The FX needed to realize their powers effectively will be easily doable on a TV budget, especially one on ABC. Smallville, on a smaller network, was able to do certain things just fine, such as super strength. It was when they had to tackle other powers like energy projection or manipulation that you could see they were stretched.