While echoing Ron and John's comments that there is no universal "best practice" here and there's only what's best for you, I'd like to propose an alternative solution that you haven't mentioned yet.
EdgeRouter does support bonding/link aggregation using 802.3ad Link Aggregation Control Protocol (LACP). However, in older EdgeRouters, this traffic was not eligible for offloading, which meant bonding (for example) 4 gigabit ports wouldn't result in 4Gbps of bandwidth. It would produce redundancy, but some bandwidth less than 4Gbps, possibly simply 1Gbps. However, according to this page, newer ER-X, ER-X-SFP, and EP-R6 EdgeRouters support offloading, so aggregating 4 gigabit ports should result in 4Gbps (or very near it, allowing for some losses).
So, in theory, if you had one of the newer EdgeRouters, and you didn't need certain mutually-exclusive protocols, and your network topology supported it, you could do the following:
- Bond X ports on the router to support XGbps of bandwidth (and also redundancy)
- Bond X ports on the switch in the same way
- Connect X ethernet cables between the bonded router ports and the bonded switch ports
- Configure your VLANs on the single bonded interface on the router and switch (I say this in a rather nebulous way; there are a lot of steps to this, clearly)
Through this configuration, all the VLANs would be able to take advantage of up to XGbps of bandwidth between the VLANs (for allowed traffic), so that you wouldn't have saturated links using all 1Gbps and bottlenecked while other links used only a few Mbps and remained essentially unitized.