Can we do this trip in reverse order?

Yes, but start with Galapagos. Going from sea level to 11,200 feet in Cusco is harder on your body than the reverse. Plus you'll want to end on the high of Machu Picchu.

Is altitude sickness really that bad in Cusco?

It hits about 50% of visitors. Symptoms include headaches, nausea, fatigue. Arrive 2-3 days early, drink coca tea, avoid alcohol first day, and consider altitude sickness medication.

Do we need a cruise for Galapagos or can we island hop?

You can island hop staying on Santa Cruz, but you'll see maybe 30% of what cruise passengers see. Cruises access remote islands and better wildlife viewing spots. Budget minimum 4-day cruise.

How to Plan a Romantic Couples Trip to Machu Picchu and the Galapagos Islands

Book this 12-14 day trip 4-6 months ahead. Fly into Lima, train to Cusco for 4 days of altitude adjustment and Machu Picchu, then fly to Quito and onto the Galapagos for 5-7 days. Budget $6,000-$12,000 total for two people depending on Galapagos cruise level.

Book flights 4-6 months ahead. Fly into Lima (LIM). Book separate flights: Lima to Cusco, Cusco to Quito, Quito to Galapagos (GPS or SCY). Return via Quito to Lima to home. Expect $1,200-$2,000 per person total.
Reserve Machu Picchu permits immediately. Buy Huayna Picchu or Machu Picchu Mountain permits online at machupicchu.gob.pe. Only 400 Huayna Picchu permits per day. Book the 7am slot for best photos with fewer crowds.
Choose your Galapagos experience. Luxury cruise: $4,000-$8,000 per person for 5-7 days. Budget alternative: Stay on Santa Cruz Island at Finch Bay Eco Hotel ($400-600/night) and do day trips ($100-200 per person per trip).
Plan 3 nights in Cusco before Machu Picchu. Stay at 11,200 feet to acclimate. Book Palacio del Inka or similar. Day 1: Rest. Day 2: Sacred Valley tour. Day 3: Cusco city. Day 4: Machu Picchu.
Book the Hiram Bingham luxury train. Splurge on the $950 per person round-trip train from Cusco to Machu Picchu. Includes gourmet meals, cocktails, and VIP access. Book 3-4 months ahead.
Get yellow fever vaccination. Required for both destinations if coming from certain countries. Get vaccination 10+ days before travel. Bring WHO yellow fever certificate.
Pack for two climates. Cusco: Cold mornings (30-40°F), warm afternoons (70°F). Galapagos: Hot and humid (75-85°F) with strong sun. Pack layers and serious sun protection.

Can we do this trip in reverse order?: Yes, but start with Galapagos. Going from sea level to 11,200 feet in Cusco is harder on your body than the reverse. Plus you'll want to end on the high of Machu Picchu.
Is altitude sickness really that bad in Cusco?: It hits about 50% of visitors. Symptoms include headaches, nausea, fatigue. Arrive 2-3 days early, drink coca tea, avoid alcohol first day, and consider altitude sickness medication.
Do we need a cruise for Galapagos or can we island hop?: You can island hop staying on Santa Cruz, but you'll see maybe 30% of what cruise passengers see. Cruises access remote islands and better wildlife viewing spots. Budget minimum 4-day cruise.