As others have said, end grain is always going to be problematic. Making breadboard ends will of course fix the problem of the color, but it's maybe not the aesthetic you're looking for.
That being said, I just want to put in a plug for Charles Neil's pre-color conditioner. I have used it on two projects now, and it really does work miracles to control uneven staining... It works great on blotchy woods for face grain (I've used it on pine and poplar), but it also works to control end-grain color differences... way better than shellac for both face and end grain. You can look up other reliable testimonies on the internet.
For my end grain application, I put a paper towel soaked in the conditioner and let it sit on the end grain for a good while to really get saturated. Then I dried, sanded, and did it again. Then, when I was staining, I was very judicious in my application of the stain on the end grain... I did multiple applications of stain on the long grain but only one and a half applications on the end grain. (The half application was done by applying it without stirring the stain first.) If you're careful, you can get an excellent color match. Of course, the texture of end grain will always be a bit different and give a different visual, but the results were excellent IMO. I wish I had pics, but I don't, and now the console table I did this on is in storage.
You can pick up the product here:
http://www.cn-woodworking.com/cn-pre-color-conditioner/
I swear I'm not being paid for this endorsement... It just really works!