I would not consider Resident Evil Outbreak and its "sequel" to be part of the main series for the following reasons:
Marvin is mentioned to have been injured during the escape of the eight survivors at the end of the "Desperate Times" scenario. It is mentioned in the Resident Evil Archives that Marvin was attacked during a blockade incident while sealing the police station.
Various changes were made to the layout of the Desperate Times scenario that were not featured in Resident Evil 2. This included the lack of a third floor, a missing door on the first floor, and a size error on the basement floor (the armory room conflicts with the parking ramp). This appears to be confusing for some.
In the scenario Below Freezing Point, several doors have been destroyed by hunters. After the survivors escape, Claire and Leon venture through the labs. These doors are not damaged during Resident Evil 2 which is very strange.
Various other changes are made to the layout of returning areas that conflict with their originals. Mixed with the fact that Outbreak was originally a twenty level game (ten levels are only featured) with branching paths, the game's storyline in itself could be deemed as being incomplete.