Ogg and Matroska both have different philosophies, and both can co-exist. Matroska is more a kitchen sink format, whereas ogg is an absolute bare bones format. Which one is better really depends on preference. Ogg is focussing on high compatibility and playability, making it ideal for content distribution, as well as streaming. Ogg is ment to become the free alternative for content distribution Matroska on the other hand is competing with MOV and Quicktime, and aiming to replace AVI and VfW/Dshow, as a general use container with a clear focus on video and audio editing.

Speaking of Ogg, there is not enough information on the container level, and too much has to be done on the decoder level, especially for editing purposes. For content distribution and streaming this approach is quite good, Although a bit more complexity could have improved Ogg's capabilities in comparison to other competing containers, aiming for the same thing, like RM, ASF and in future mainly MP4, but it was decided to keep it as simple as possible, and there are of course some very nice advantages of doing that, especially with respect to Xiph's opensource approach.

Matroska, unlike Ogg is complex. Seeking in matroska is fast as compared to that in Ogg. You can use features like menus, chapters etc in Matroska.