Shopify keeps 18% of your margin and you don't notice
$99 subscription, 2.4% transaction fee, essential apps $200, premium theme $300, cart abandonment $50... When you add it all up, Shopify keeps almost 1 in every 5 dollars you sell.
The math they don't teach in onboarding
Your store sells $50,000 USD/month. You feel things are going well. Let's do the math: Shopify Plus $2,300/mo, loyalty app $300/mo, reviews app $100/mo, upsell app $200/mo, transaction fees 2.4% = $1,200/mo, amortized premium theme $50/mo, domains/SSL $30/mo. Total: $4,180/mo. On $50,000 sold, that's 8.3% direct. And that's BEFORE gateway fees and return costs.
The "quick start" argument no longer applies
Shopify's main selling point was "launch in 2 weeks". Today a custom e-commerce with modern templates (Next.js Commerce, Medusa, Saleor) also launches in 4-6 weeks. The difference: in 18 months your Shopify store costs double. Your custom store has already paid the build and keeps costing the same.