Two powered subs with bookshelf speakers or two floor-standing speakers?

This is kind of an impossible question to make good recommendations and really requires knowing what equipment is in both systems.  But, to me, any girl who rocks JBLs is worth marrying.  Just sayin’.  
That said, and in very general terms, if you’ve got a low budget then monitors and two decent subs should be better as you’re getting more near full range and cheaper floor-standing speakers will likely have cabinet-resonance issues that can be less invasive in monitors given their smaller size.  Again, far too many variables here to make any comfortable recommendations other than just some blind general statements.  The more info on equipment, budgets, room size, tastes in sound/music you can give the better.

I just transitioned from BS with subs to floor standers (with and without subs). IMO, Subs, unless they are really good/expensive are often not great for music other than sub 40 hz thump or to feel the music (and in that capacity they make a huge improvement for some music). I found the best, most cohesive sound with just two floor standards (F208). The subs were even muddying up the sound on those and I had to keep moving them and adjusting them. I have finally found settings/locations where they supplement the sound and not overlap the sound from the floor standers. Expensive subs designed for music are easier to integrate but I don’t have $4200 to drop on subs right now.

Aesthetic considerations (room decor circa 1915) and small size 15' x 15' necessitated use of small bookshelf B&W 805's and subs REL T7/x's to blend/hide the speakers in the background.  RELs in the corners, B&W's literally on bookshelves.  Less than ideal, however toeing the speakers and fine tuning bass volume and crossover has yielded a very nice soundstage and a very musical sounding room.  My brother who has Monitor floor standing speakers used my room as the bench mark for his HiFi system.  So yes it can be done to good results.

I had a number of very good bookshelf speakers (B&W 805D, Harbeth 30.2) and subwoofers (REL, SVS) in different rooms. Sound was very good but not even close to floor standers I now use (Wilson, Spatial Audio). As others stated above, integrating subs with bookshelfs can be difficult. I am convinced that using floor standers is much better option.

-GAR

You’ll never use your bookshelves again if you get a good pair of floorstanders. My Tekton Pendragons give you deep solid lows...smooth mids and slightly rolled off highs but detailed. Very musical and $2500 pr. Get the 7 tweeter array option.

I’ve often considering going from two stand mounts, two subs (current setup) to two floor standers, two subs but I hesitate because my current setup sounds absolutely amazing as is and I also like having one of the two subs as a near field sub, just to the left of my listening position. Works great in my room this way. The other sub is in the corner behind my right channel stand mount speaker. My point is that bass is sometimes better dispersed in the room if you can play around with the sub placement rather than having it tethered to you speaker as it is in a floor standing speaker.  

It may depend on what you define as bookshelf. A 7” or 8” woofer can go low enough to make the sub truly a subwoofer. A 4” or 5” woofer usually cannot, so the “sub” is really covering a range into the midbass where its presence is more discernible and thereby harder to blend in. The other issue is placement. Not every room affords you the option of putting speakers where they can sound their best.  Having a sub can either ease or worsen this problem…

in theory, you have more flexibility with bookshelf speakers and subs. In reality, it's much harder to get it right.

The easiest route is powered floorstanding speakers. But who wants it easy? 

it simply depends on too many factors to have an opinion on the generality

if there is a generality, it would be that well integrated subs always add to the quality of sound of most systems

You can make bookshelf speakers with subs work, but it is harder to do.  Some like it if they are the type that wants way more bass than the artist put on the original recording.  I've heard one great system in this configuration using Raidho and REL, about $30k in speakers.  

Floorstanding is much easier to make sound good.

YMMV.

Jerry