1. Depends entirely on the content of the site, the brand, etc. Generally speaking I prefer more-subdued colour schemes, as it makes it easier to take in information.
2. This again depends on the type of site and content is hosts. I've personally never used one of those pop-ups that lets you ask questions about a product or service. I think I have used them to speak to a customer service advisor on a few sites as it's often quicker than a support ticket. Many online retail sites have the ability to ask questions about specific products, though whether or not you get a response in a timely manner, or even at all, is another question.
For a smaller retail store it's perhaps worth adding an enquiry form to each product listing so you can ask questions about this item to the retailer directly. I designed and built a property listing site for a client a while back and this was basically how users made contact to arrange viewings, just a form that spits out an email with the user's details and property reference number.
3. Can you clarify your question? I think I know what you mean so I'll attempt to answer:
As a designer I like sites that push the boundaries and expectations and provide users with an experience that differs from what they're used to. In practice, this can be difficult to implement, especially when you consider mobile versions of said site, and usability and logical navigation often wins out over a completely abstract idea. We've come to develop a language for navigating screen content, and deviating too far from this can lead to usability problems.
As an example, an original idea I had for a portfolio redesign was a site that was infinitely draggable, with content scattered about this space. Turns out that this idea was ironically better suites to touch devices as the method of navigation was natively suited to touch screens, but it just wouldn't work on mobile due to the restrictive size of the screen. The tablet and desktop version got a lot of positive feedback, but the mobile version was hard to navigate, and a total pain to develop so I dropped it.
Linear layouts are often a lot quicker to design and build responsively, but can lead to boring or expected designs if you're not careful.