Customization is lacking. Font sizes, background colors for form fields, adding images to forms and reports, etc. These are all big issues for us. We keep working around it but it's not ideal and we have to use a lot of hacks and a lot of unnecessary development time that could be better spent in other areas. Not being able to have a customized header and footer has been really difficult. We have to use a lot of forms for our reports because they are easier to customize but when you email and print they don't look good. We've had to lower the quality of our deliverables to our clients which we get complaints on frequently.
Notification emails only allow for a predefined user list or one email. We often have to send a notification to multiple people. So rather than everyone getting the same email at the same time, we have to send out separate emails or email ourselves then forward so everyone can respond. Once again, extra time and effort that could be better spent providing services to the community (we're a non-profit).
Lack of integration. You can use third parties but the cost becomes too much especially as a non-profit. It's hard to justify spending thousands a month on integrations for our team when we work off of grants and charitable donations. So being able to integrate with Outlook or Word to get around the lack of customization is not affordable and then you're dependent on a third party as well as Quick Base.
Inability to perform searches on the data directly. Having used Access, SQL, and MySQL it's very limiting being restrained by Quick Base. Report links and lookup fields work but it's ridiculous that the workaround is including (sometimes hundreds of) lookup fields. This, of course, adds to the time of development needed and also slows down the tables.
Not having many-to-many relationships. While the hacks work, for the most part, the amount of extra development time that is needed to tweak the tables, the forms, and the reports adds up. This is also why reporting can only come from child up which once again, you have to spend so much time on hacks to display the data you want.
Lack of instructions available. While Quick Base university is quite good, doing a google search usually entails wading through a bunch of Quick Base community questions. At the beginning of development and for simple things, it's always easy to find the answers but as development continues and more customization to your company's business model is required it gets harder to find solutions. I'm sure as time goes by it'll be better as there will be more information available.