There will always be growing pains as a company evolves, and such as the combination of classic and threads, this is no different. How thin should a company spread themselves? A hosted product, a hosting service for downloadable products, a php/mysql product, a legacy product...
All of that equates into a lot of money spent sparingly on a lot of different areas, let alone the vast array of support knowledge required to support all areas. You will always have your customers who are threads fans, you will have your classic fans, and there is no denying that. But at what cost will this continue to thrive? All of the additional administrative and logistical issues caused by multiple platforms in essence cause the price of each product to be higher than competitors. This higher cost may yield a small number of satisfied clients, but in the end, costs the company a great deal of money because someone can go down the block and get another forum that does essentially the same stuff but for a much more affordable price. This in turn makes it even more difficult for this company to compete, so prices cannot improve due to the volume of sales.
That is why this merger is so great. Prior to this, you had teams devoted to each platform individually, on two very different technologies and philosophies, each trying to please two niche groups of people. In essence, everyone wants the same thing, a great message board with great features, great speed, great support, and a thriving mod community. By separating each group, you have segmented a community that are longing for the same things, costing not only development time, but revenue because of the very different products.
Once one product is finalized, with the benefits of both classic and threads, you will have more people focused on ONE product, and you will have a development community that will more than double in size, and overall, simply a better product that can compete more readily in the online community market.
Sure, I'm the first one to say there are some things in threads I don't like compared to classic, just as there are some classic things I don't like which threads does. Some of my users have trouble with threads compared to classic or your vb/phpbb sites, but others really like threads compared to those. You will never please everyone 100% of the time, but by combining the best of both and focusing the strengths on one product, this really is a win-win for everyone involved.