1. Its Expensive
A SharePoint implementation doesn't have to be expensive. The most commonly used features such as:
These all come standard with Windows SharePoint Services (WSS).
WSS comes free with Windows Server 2003 and 2008. You don't even have to
purchase a SQL server licence.
2. It's not user friendly
Because SharePoint is easy to get up and running and is relatively inexpensive, many organisations install it and provide no training or instruction to their staff.
Like any highly functional software, SharePoint can introduce a lot of new concepts and so there are certain steps that should be taken by every organisation implementing SharePoint:
Assign a SharePoint champion(s).
Someone who has a good understanding of SharePoint from a users perspective and can help with day to day issues.
Someone to help manage change in an organisation, often with resistance from users.
With proper planning many of the common usability issues users experience when they first encounter sharepoint can
be greatly reduced or even removed. E.G Hiding features that are unnecasary or by creating shortcuts to the most commonly used features.
3. It doesn't look good always looks like SharePoint.
When it comes to the look and feel of SharePoint there are really 2 different SharePoints.
There is the Web Content Managment Side (WCM) and the Enterprise Content Management (ECM) side.
The good news is that the WCM side can be made to look however you choose.
Some of the best examples can be found here - http://www.wssdemo.com/Pages/topwebsites.aspx
The ECM side which is more commonly used for intranets is easy to brand, harder to customise but can still be done so with a bit of effort.
Examples of what can be done can be seen on sites such as sharepointpackages.com
4. It's only a document management system
Although the fantastic Document Management functionality is what initially attracts most organisations to SharePoint,
Document Management is only skimming the surface of SharePoint's capabilities.
Some of the out of the box features are
and much more
5. It can be installed and configured by your IT dept even if they have no
SharePoint installations can be done by anyone with IT experience but there are likley to be many best practices that will get overlooked.
Examples are incorrect permissions, sub optimal performance configuration, planning for future growth and correct back up procedures.