The problem with the bakufu (well, one of the problems) is that it was highly resistant to change and meaningful reforms. They were better at adopting new military tactics and technology than they were reforming the internal administration of Japan. It was an increasingly shaky (due to large amounts of disgruntled samurai), unfair system that had worked well at one point in time but was increasingly becoming fragile, and policymakers mostly just resorted to vague Confucian decrees in an attempt to paper over the cracks. I don't think the bakufu surviving is impossible, but it would probably require a dynamic group of reform-minded leaders within the system to pull it off, and it's a bit hard imagining such people rising to the top (there were members of the government who were more forwards thinking, but never enough).
That being said, lets say the bakufu does pull through, at least in the short term. Rather than winning the Boshin War I think a better POD would be them successfully suppressing Satsuma and Choshu in the years leading up to the war. It's not that hard to imagine something like the Second Choshu Expedition being a success. Many of the military reforms of the Meiji government had their roots in late bakufu policies so there's not really a big change there. A major question mark would be how the bakufu handles the samurai class. The Meiji government abolishing the feudal privileges of the samurai was a major step towards economic modernization. Given that the bakufu drew its legitimacy in part from being the top samurai they may have a tougher time doing that. On the other hand, the samurai are the class most responsible for the downfall of the bakufu, so maybe they'd take stronger action. As it turns out having a large class of well-educated, disgruntled men with militaristic ideals is something that can lead to a good deal of political instability.
I think a surviving Tokugawa government would have a much weaker economy than Meiji Japan and would thus not be in the position to embark upon a massive expansionist program. They could keep Russia "at bay" through an alliance with Britain and/or France but they won't be a major continental power. If you set their economy back by, say, 10-20 years you already make it much harder for Japan to accomplish what they did OTL. Japanese victory in the First Sino-Japanese War for example wasn't foregone conclusion - many observers at the time expected China to win. Slow down Japan's industrialization and they probably never even embark on such a war in the first place. I also think that without major reforms the bakufu would fall eventually. Pre-Meiji Japan already had a high rate of urbanization and literacy for an agrarian society, with both merchants and samurai forming a politically aware urban middle class. This cosmopolitan middle class is only going to become wealthier and more politically aware as trade with the outside world picks up, and they're going to start wondering why they're stuck being ruled by some stuffy old families who just happened to win a war a few centuries ago.