This is from the documentation for the V2 tool on Colibri's website.
in the new version anyone can create chains and add it to the RBT, but the key search will only use chains that are listed in a small (non text) file called ChainAuthor.map. If you have created a chain file and share the download link to our community than I will add the chain file name to the ChainAuthor.map file and upload it regularly.
This is a message you'll see on his site.
Don't create new RBC2, RBC3, RBC4 chain files, because no update to the ChainAuthor.map is planned, since dvbn.happysat.org has been closed on Sep, 25th 2015.
So, the answer is yes. There's a very good reason to continue using version 1. You or anyone else can continue to make chains for the version 1 tool and the success rate can grow. You or anyone else can also continue to make chains for version 2, but since they must be added to the Chain author map file and Colibri has stated that he will no longer update this file, to do so is useless. So, that means there's a good reason to stick with version 1 and not go to version 2 .
If you read the documentation for version 2, the same documentation I copied the first quote from, you'll see the main purpose of version 2 was to increase the speed at which a CW could be found. The goal there was to get it under 10 seconds. It seems the motivation for this was to possibly target systems where the control word changes every few seconds and the goal was to develop code and tables that could possibly be adapted to those type systems. However, for fixed cw systems, like biss, V1 is probably what you should stick with.
If it says you need a bigger table, then you need a bigger table with more chains. You can make them yourself or you can download them. The pascal cards are fast at making chains.
Note however, the rainbow table method is not perfect. The whole approach relies on filling bytes being added to the packets. If a stream doesn't have these filling bytes or if the streams that do have filling bytes, like the audio stream, are left unencrypted, this method cannot work. when that happens you will know it because there will be no crypt8 found in the stream. For those type of streams only a bruteforce will work.