Is it possible to be exempted from the wetlands requirements under this credit if we protect or restore equivalent wetlands elsewhere?

No, this is not an accepted compliance path. LEEDuser's experts agree that you are unlikely to get traction with this due to the immediate and unsustainable impacts on local ecosystems and hydrology.

The project site is classified as "prime farmland," but is in a developed area with buildings all around. Can I still comply with this credit?

LEED does not have published exceptions to the prime farmland requirement. You would need to submit a CIR to get an official ruling.

However, some projects have had success contacting the local USDA representative and requesting an evaluation to get an exemption due to the low probability that the land could be usable for agricultural purposes.

What am I required to submeter for this credit?

For EAc5.1, there are no specific requirements. In your M&V plan, you will identify the uses you will submeter or monitor in order to confirm your energy savings. If you are pursuing Option 2 (Energy Conservation Measure Isolation), it may make sense to directly submeter the equipment in question. For the related tenant M&V credit, EAc5.2, tenant spaces must submetered or independently metered by the electric utility.

How can I choose between Option 1 (Calibrated Simulation) and Option 2 (Energy Conservation Measure Isolation)?

Option 2 is only appropriate for measures that are simple to analyze and that have few or no interaction with other building systems. For most new buildings and gut rehabs, there will be significant interaction between systems (such as lighting and HVAC) and Option 1 (simulation) will be the best option.