Your 3550G currently hosted at most 12 connections at 1Gbps. With the same count of connections, the 3560E should not have any issues. In fact, the switching capacity of 3550G-12 was rated at 17.0 Mpps while the 3560E is rated at 101.2 Mpps and its switching fabric is rated at 120 Gbps. See:
The 3560E-48PD-S only has an IP Base feature set. If you were running an EMI-feature-set on the 3550 it could be that you lose some features with the new switch. You should check your config if the new switch supports all features that you are already using. But the IPBase can be upgraded to IPServices through Software-Activation.
As a short summary the software-description of the 3560E:
The Cisco Catalyst 3560-E Series is available with either the IP Base or the IP Services feature set. The IP Base feature set includes advanced quality of service (QoS), rate-limiting, ACLs, and basic static and Routing Information Protocol (RIP) routing capability. The IP Services feature set provides a richer set of enterprise-class features, including advanced hardware-based IP unicast and multicast routing -- Enhanced Interior Gateway Routing Protocol [EIGRP], Open Shortest Path First [OSPF], Border Gateway Protocol [BGP], Protocol Independent Multicast [PIM] and IPv6 routing such as OSPFv3 and EIGRPv6
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One issue you might bump into, depending on device configuration, the 3560/3750 series often have interface drops that you might not see on a 3550. The two series manage their interface buffers differently.
You might also need to set the SDM template to your needs.
We are pleased to announce availability of Beta software for 16.6.3. 16.6.3 will be the second rebuild on the 16.6 release train targeted towards Catalyst 9500/9400/9300/3850/3650 switching platforms. We are looking for early feedback from custome...