we are planning to push out additional financial institution support in the near future even with the current download method
You're never going to cover everything. Also keep in mind that even if you're targetting US users, you're going to have non-US users -- who have non-US investment accounts, and often e.g., pension plans which don't have online access at all.
Point taken. Manual entry is definitely a proper catch-all. The Yodlee service gets pretty close, although perhaps not as wide reach internationally (I believe they support some banks in India) or pensions.
You're never going to cover everything. Also keep in mind that even if you're targetting US users, you're going to have non-US users -- who have non-US investment accounts, and often e.g., pension plans which don't have online access at all.