According to the Guildpact FAQ, Replicate means:
"As an additional cost to play this spell, you may pay [cost] any number of times" and "When you play this spell, if a replicate cost was paid for it, copy it for each time its replicate cost was paid.
So, here's how it goes. You play your spell, and you decide whether or not to replicate it. If you do decide to replicate it, then you figure out what you should be paying. Thus, if you decide to replicate once, you need to pay RR. NOW you apply Trinisphere and see what you would be paying. In this case, you're wanting to pay RR, but Trinisphere sees that this is less than 3, so it bumps it up to 1RR.
Here's a table of what it costs to do stuff with Shattering Spree with 3Sphere out there:
Destroy 1 artifact = 2R
Destroy 2 artifacts = 1RR
Destroy 3 artifacts = RRR
Destroy 4 artifacts = RRRR
Trinisphere doesn't look at mana cost. It looks at what you're paying for a spell, after any cost increasers are applied. This is why it only costs 3 to play Mox Sapphire while Trinisphere and two Sphere of Resistance are out there.
