Starting a complete new chipset for a basically different system is not quite easy. The manufacturers of chipsets (or motherboards) don't get the chance to play around with the cache timings in Slot-1 systems any more, so they have to try optimizing the bus and memory performance. In the last months and even years Intel has proved this to be one of their best fields. That's why I'm not very surprised that the first generation of non-Intel Slot-1 chipsets wouldn't be able to beat them.
In Quake II, which is very bandwith-sensitive, both the 5600 and the Apollo Pro chipset are clearly slower than the 440BX, which shows a little bandwidth lack of the newcomers. With Incoming the difference is not that big. The Winstone runs do not differ that much, since large parts of the program's code is written to optimally take advantage of the fast L2 cache. The Highend Winstone requires a lot of CPU power and makes the differences clear again.
There's still a lot of work to do for both the chipset and motherboard manufacturers. As you have seen now, the alternative chipsets can not reach for the crown. But they are a quite cheap alternative for all who want to have a Slot-1 system (with a 66 MHz CPU, e.g. Celeron A) which is capable of running all available CPUs.
I personally wouldn't want to chose between one of the newcomers and a BX board (as power user I would take the BX board), but getting a Apollo Pro board instead of a EX or LX motherboard is now a real alternative. An EX board has only few expansion slots and doesn't run at more than 83 MHz FSB. An Apollo Pro based motherboard may have twice as much slots, one or two more DIMM sockets, 100 MHz capability, ECC support and the option of running the memory at the AGP clock at safe 66 MHz. And if you would get both boards for the same price...
On the one hand neither VIA nor SiS are able to offer a chipset which would beat Intel's BX, but on the other hand lots of new board with both new chipsets will be available soon and poach market shares in the low cost sector which Intel was originally trying to regain.