Hello, quick intro of myself: I'm a Canadian student that is currently doing a PhD at Caltech in Planetary Science (related to Physics but not in the Physics department!). I did my undergrad at UBC and my Masters at Queen's (both in Astronomy) and I hope what I say can be helpful:
While the majority of Canadians I've met at big name US schools come from the "big 3" Canadian schools (UBC, Toronto, McGill; in no particular order), there definitely exists other students at top US schools from smaller Canadian schools. I know of students from Queen's (still a big Canadian school though), Western, York, and McMaster at top US schools. I'm sure there are others. I also think the reason why I don't hear about these students from smaller Canadian schools is just that there are fewer students in these programs so it's harder to find them.
I think the "brand name" of a school does play a role even when you have good GPAs etc. In Canada, grades are a bit more standardized -- i.e. the conversion from X% to letter grade is common across most science programs in Canada, but this isn't always true in the US. Also, there is different grading standards at different programs, so a 90% average at one school might be valued differently than a 90% average at another school.
But I agree with you that by far, the most important aspect is what research experience you can get at your undergrad school. Macleans magazine splits up Canadian schools into 3 categories:
"Medical/Doctoral" which means "research intensive schools": http://oncampus.macleans.ca/education/2 ... -doctoral/
"Comprehensive" which means slightly less research intensive: http://oncampus.macleans.ca/education/2 ... rehensive/
and "Primarily Undergraduate" which I would say are less geared towards preparing students for grad school, but that is a generalization! http://oncampus.macleans.ca/education/2 ... rgraduate/
The one exception for Physics/Engineering is that Waterloo appears on the second list but it really is a top notch research university for some fields.
In my opinion, if you want to go to the top US schools, you should aim for schools in the top half of that first list, as they have the reputation for research worldwide. Maybe the top few schools in the second list would be okay too. However, your research opportunities will be more limited.
That said, you should know that you aren't limited to your undergrad school for research opportunities. NSERC offers USRA (Undergraduate Student Research Awards) which will help pay for 16 weeks of full time research (usually in the summer). You would apply for USRA positions directly to the school you want to work for, e.g. one of the top schools where there are more opportunities.
However, there is usually a quota for the amount of USRAs awarded to students from different schools. Also, there is a lot of advantage to being immersed in an environment where there is a lot of research going on. And, having profs that are doing exciting research is a different experience than profs who are primarily involved in teaching. It's true that the quality of instruction at research intensive schools is lower than smaller schools and that you will probably not be as noticed by profs unless you're a star student, though.
Fortunately, most Canadian schools are relatively inexpensive, especially compared to US schools. To save money, you might want to live closer to home so that might limit your choice of undergrad. So, if you are really certain that you want to do graduate studies in the US and want to get as much research experience as possible in undergrad, I'd recommend sticking to the "medical/doctoral" list and trying to find the best school you can get into / can afford (scholarships are available too!). But keep in mind that for many students, priorities may change during undergrad. Another thing you can look out for when researching undergrad school is to look for "co-op work education" programs. UBC has one. In a co-op program, you spend 4 years of school in the classroom and 1 year plus 2-3 summers doing full time work in your field. They pay you pretty well -- I earned enough money during my co-op work months to pay for my entire tuition. And you get excellent research experience. When I graduated from UBC, I had 16 months of full time research experience in 2 different research groups at UBC plus my undergraduate research thesis. Working on a project full time for 8 months lets you make a ton of progress and really helps you get to the stage where you can publish the work and present at conferences.
Therefore, I would very strongly recommend that you keep your research opportunities in mind when picking a undergrad school if a top grad school is indeed your goal. I strongly recommend co-op programs -- they help you pay your tuition and the experience you get is well worth that extra year. Co-op programs are competitive to get in, but when I applied at UBC for the Physics co-op program, there were few enough applicants that you just have to meet the minimum standards. However, there may now be a competitive process involving interviews etc. to get in. Also, as part of the co-op program, you attend workshops that teach you useful skills such as getting a job outside of academia, if you choose to go that route!
Hope that was helpful