Which business model is the best for system integrator company ?

3) Business development manager for sales and presales and separate department for projects

It all depends on the customer segment and how they perceive value. 

Some business take a pure technology view and don't get stuck on brands. However, brands encourage partners for certifications and expect numbers and have their own methods and guidelines to approach markets.

Generally speaking, it is a knowledge business and specialists which deeper insights in account management, sales process, technical presales activities , implementation skills and later support management. 

However, you slice it and dice it, the customer always needs a single point of contact and the ability of the account manager to coordinate resources is the key to the success. If you organise the business which helps the account manager in this process, it helps.

Best approach is to take continuous customer feedback since people change and their capabilities will also get affected.