[swombat]

Setting up your own server gives you full flexibility as to your application architecture/tech stack. Want to go with Redis? Tokyo Cabinet? MogileFS? S3? A pile of files in a zillion small directories? something else? Your choice.

If your startup has any challenging technical elements, I think having 100% full control over your app architecture is quite important. You can live without it, but it's a potentially costly trade-off.

[angilly]

FWIW, judging by "My team does not have experience in setting up a server" I doubt OP is going to be playing with any of that stuff.

[swombat]

Granted, but if your team doesn't have experience setting up a server, I question whether they have the required skills to run a startup's technology. A startup CTO should be able to set up a server reasonably quickly, effectively, and securely...

[boltofblue]

Heroku doesn't stop you using Mongo, Redis or S3. They actually promote these things.